Starting phenix.real_space_refine on Fri Aug 7 13:11:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ukd_64235/08_2026/9ukd_64235.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ukd_64235/08_2026/9ukd_64235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ukd_64235/08_2026/9ukd_64235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ukd_64235/08_2026/9ukd_64235.map" model { file = "/net/cci-nas-00/data/ceres_data/9ukd_64235/08_2026/9ukd_64235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ukd_64235/08_2026/9ukd_64235.cif" } resolution = 3.71 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= 0.002 sd= 0.035 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 18 5.49 5 Mg 4 5.21 5 S 88 5.16 5 C 13322 2.51 5 N 3799 2.21 5 O 4024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 21255 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2377 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 12, 'TRANS': 287} Chain breaks: 1 Chain: "B" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2467 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 12, 'TRANS': 299} Chain: "C" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2458 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 12, 'TRANS': 298} Chain: "D" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2506 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 12, 'TRANS': 305} Chain: "E" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2522 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 12, 'TRANS': 307} Chain: "F" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2506 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 12, 'TRANS': 305} Chain: "G" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2421 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 10, 'TRANS': 293} Chain: "f" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1684 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain: "I" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2124 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 8, 'TRANS': 260} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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, 'ATP': 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, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.61, per 1000 atoms: 0.22 Number of scatterers: 21255 At special positions: 0 Unit cell: (127.036, 126.338, 145.882, 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 88 16.00 P 18 15.00 Mg 4 11.99 O 4024 8.00 N 3799 7.00 C 13322 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: 1.80 Conformation dependent library (CDL) restraints added in 908.1 milliseconds 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5016 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 28 sheets defined 45.7% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 17 through 22 removed outlier: 3.920A pdb=" N VAL A 21 " --> pdb=" O SER A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 64 Processing helix chain 'A' and resid 79 through 88 Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.658A pdb=" N ILE A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 224 through 233 removed outlier: 3.603A pdb=" N ILE A 228 " --> pdb=" O ASN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 261 removed outlier: 3.701A pdb=" N GLU A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 250 " --> pdb=" O ASN A 246 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 283 removed outlier: 3.801A pdb=" N VAL A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 Processing helix chain 'A' and resid 295 through 298 removed outlier: 3.608A pdb=" N CYS A 298 " --> pdb=" O LEU A 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 295 through 298' Processing helix chain 'A' and resid 302 through 312 removed outlier: 3.851A pdb=" N VAL A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.666A pdb=" N VAL B 21 " --> pdb=" O SER B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 63 Processing helix chain 'B' and resid 77 through 89 Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 127 through 133 Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 204 through 210 removed outlier: 3.515A pdb=" N MET B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 234 removed outlier: 4.377A pdb=" N ASN B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 262 Processing helix chain 'B' and resid 269 through 284 removed outlier: 3.868A pdb=" N VAL B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 298 Processing helix chain 'B' and resid 299 through 315 removed outlier: 4.555A pdb=" N ALA B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N THR B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 50 through 64 Processing helix chain 'C' and resid 76 through 89 Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 126 through 134 removed outlier: 3.603A pdb=" N TRP C 130 " --> pdb=" O GLY C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 159 removed outlier: 3.603A pdb=" N MET C 151 " --> pdb=" O ARG C 147 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL C 157 " --> pdb=" O VAL C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 211 removed outlier: 3.904A pdb=" N MET C 208 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 238 through 262 Processing helix chain 'C' and resid 269 through 283 removed outlier: 3.903A pdb=" N ALA C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 295 through 298 Processing helix chain 'C' and resid 299 through 315 removed outlier: 4.304A pdb=" N ALA C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N THR C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 22 Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.606A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 134 removed outlier: 3.648A pdb=" N TRP D 130 " --> pdb=" O GLY D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 147 through 156 removed outlier: 4.832A pdb=" N VAL D 153 " --> pdb=" O ASP D 149 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE D 154 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG D 156 " --> pdb=" O PHE D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 221 through 233 Processing helix chain 'D' and resid 238 through 261 Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 295 through 298 Processing helix chain 'D' and resid 302 through 314 removed outlier: 3.547A pdb=" N VAL D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 22 Processing helix chain 'E' and resid 50 through 64 Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 127 through 134 Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 204 through 209 Processing helix chain 'E' and resid 221 through 233 Processing helix chain 'E' and resid 238 through 262 Processing helix chain 'E' and resid 269 through 283 Processing helix chain 'E' and resid 285 through 294 Processing helix chain 'E' and resid 295 through 298 Processing helix chain 'E' and resid 302 through 314 Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'F' and resid 51 through 63 Processing helix chain 'F' and resid 76 through 89 Processing helix chain 'F' and resid 102 through 108 removed outlier: 3.501A pdb=" N LEU F 106 " --> pdb=" O SER F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 133 Processing helix chain 'F' and resid 142 through 146 removed outlier: 3.916A pdb=" N GLY F 146 " --> pdb=" O TYR F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 159 removed outlier: 4.068A pdb=" N ARG F 156 " --> pdb=" O PHE F 152 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL F 157 " --> pdb=" O VAL F 153 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU F 159 " --> pdb=" O GLN F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 211 removed outlier: 3.815A pdb=" N MET F 208 " --> pdb=" O ASN F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 231 Processing helix chain 'F' and resid 233 through 237 removed outlier: 3.939A pdb=" N GLN F 237 " --> pdb=" O LYS F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 262 Processing helix chain 'F' and resid 269 through 282 Processing helix chain 'F' and resid 286 through 294 Processing helix chain 'F' and resid 295 through 298 Processing helix chain 'F' and resid 302 through 314 removed outlier: 3.820A pdb=" N VAL F 306 " --> pdb=" O GLU F 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 353 removed outlier: 3.666A pdb=" N ARG G 342 " --> pdb=" O ALA G 338 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU G 343 " --> pdb=" O GLU G 339 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG G 344 " --> pdb=" O LEU G 340 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE G 346 " --> pdb=" O ARG G 342 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN G 350 " --> pdb=" O PHE G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 369 removed outlier: 3.626A pdb=" N GLN G 366 " --> pdb=" O ASN G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 395 removed outlier: 4.240A pdb=" N VAL G 395 " --> pdb=" O LEU G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 449 removed outlier: 4.230A pdb=" N THR G 433 " --> pdb=" O GLY G 429 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL G 434 " --> pdb=" O ARG G 430 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU G 442 " --> pdb=" O CYS G 438 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA G 443 " --> pdb=" O ALA G 439 " (cutoff:3.500A) Processing helix chain 'G' and resid 466 through 476 Processing helix chain 'G' and resid 498 through 503 Processing helix chain 'G' and resid 504 through 506 No H-bonds generated for 'chain 'G' and resid 504 through 506' Processing helix chain 'G' and resid 510 through 514 Processing helix chain 'G' and resid 521 through 534 removed outlier: 3.522A pdb=" N LEU G 531 " --> pdb=" O ALA G 527 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY G 533 " --> pdb=" O GLN G 529 " (cutoff:3.500A) Processing helix chain 'G' and resid 553 through 558 removed outlier: 3.938A pdb=" N VAL G 557 " --> pdb=" O THR G 554 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN G 558 " --> pdb=" O LEU G 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 559 through 563 removed outlier: 3.872A pdb=" N LEU G 563 " --> pdb=" O GLY G 560 " (cutoff:3.500A) Processing helix chain 'G' and resid 564 through 578 removed outlier: 3.602A pdb=" N GLU G 575 " --> pdb=" O ILE G 571 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR G 576 " --> pdb=" O GLU G 572 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG G 577 " --> pdb=" O GLU G 573 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER G 578 " --> pdb=" O ILE G 574 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 34 removed outlier: 3.630A pdb=" N ILE f 29 " --> pdb=" O PHE f 25 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG f 34 " --> pdb=" O THR f 30 " (cutoff:3.500A) Processing helix chain 'f' and resid 68 through 89 removed outlier: 3.765A pdb=" N ALA f 73 " --> pdb=" O ALA f 69 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY f 79 " --> pdb=" O THR f 75 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN f 86 " --> pdb=" O MET f 82 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG f 88 " --> pdb=" O LEU f 84 " (cutoff:3.500A) Processing helix chain 'f' and resid 90 through 97 removed outlier: 3.570A pdb=" N HIS f 94 " --> pdb=" O ASN f 90 " (cutoff:3.500A) Processing helix chain 'f' and resid 101 through 124 removed outlier: 3.532A pdb=" N ILE f 119 " --> pdb=" O ARG f 115 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY f 120 " --> pdb=" O VAL f 116 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA f 121 " --> pdb=" O GLU f 117 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA f 123 " --> pdb=" O ILE f 119 " (cutoff:3.500A) Processing helix chain 'f' and resid 127 through 142 Processing helix chain 'f' and resid 149 through 153 Processing helix chain 'f' and resid 154 through 168 removed outlier: 3.994A pdb=" N ALA f 158 " --> pdb=" O PRO f 154 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS f 166 " --> pdb=" O LEU f 162 " (cutoff:3.500A) Processing helix chain 'f' and resid 185 through 191 Processing helix chain 'f' and resid 194 through 201 Processing helix chain 'f' and resid 204 through 219 removed outlier: 4.500A pdb=" N ARG f 210 " --> pdb=" O GLN f 206 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR f 211 " --> pdb=" O ALA f 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 344 removed outlier: 4.304A pdb=" N LEU I 340 " --> pdb=" O ASP I 336 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP I 341 " --> pdb=" O GLU I 337 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ARG I 342 " --> pdb=" O ALA I 338 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU I 343 " --> pdb=" O GLU I 339 " (cutoff:3.500A) Processing helix chain 'I' and resid 347 through 351 Processing helix chain 'I' and resid 356 through 365 removed outlier: 4.088A pdb=" N ALA I 362 " --> pdb=" O VAL I 358 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASN I 363 " --> pdb=" O GLY I 359 " (cutoff:3.500A) Processing helix chain 'I' and resid 429 through 449 removed outlier: 3.968A pdb=" N ARG I 448 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N CYS I 449 " --> pdb=" O THR I 445 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 475 removed outlier: 4.319A pdb=" N TRP I 472 " --> pdb=" O SER I 468 " (cutoff:3.500A) Processing helix chain 'I' and resid 501 through 506 removed outlier: 4.254A pdb=" N ASN I 505 " --> pdb=" O ARG I 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 529 removed outlier: 4.040A pdb=" N ALA I 523 " --> pdb=" O ILE I 519 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU I 524 " --> pdb=" O ASP I 520 " (cutoff:3.500A) Processing helix chain 'I' and resid 553 through 557 removed outlier: 4.026A pdb=" N SER I 556 " --> pdb=" O SER I 553 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL I 557 " --> pdb=" O THR I 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 553 through 557' Processing helix chain 'I' and resid 561 through 570 removed outlier: 3.518A pdb=" N HIS I 566 " --> pdb=" O TYR I 562 " (cutoff:3.500A) Processing helix chain 'I' and resid 571 through 576 Processing helix chain 'I' and resid 607 through 609 No H-bonds generated for 'chain 'I' and resid 607 through 609' Processing helix chain 'I' and resid 610 through 618 removed outlier: 3.552A pdb=" N SER I 617 " --> pdb=" O GLU I 613 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU I 618 " --> pdb=" O GLN I 614 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 186 removed outlier: 7.986A pdb=" N ALA A 185 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL A 69 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 96 removed outlier: 3.559A pdb=" N VAL A 139 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 95 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP A 141 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 111 removed outlier: 3.606A pdb=" N LYS A 109 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A 124 " --> pdb=" O LYS A 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 94 removed outlier: 6.433A pdb=" N VAL B 93 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU B 138 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N THR B 184 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE B 140 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N MET B 68 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.814A pdb=" N LYS B 109 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS B 124 " --> pdb=" O LYS B 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 113 through 115 Processing sheet with id=AA7, first strand: chain 'C' and resid 14 through 17 removed outlier: 3.930A pdb=" N THR C 14 " --> pdb=" O ALA C 32 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 16 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL C 30 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 92 through 96 removed outlier: 3.566A pdb=" N VAL C 93 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU C 138 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR C 184 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE C 140 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL C 67 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ALA C 185 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL C 69 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N MET C 68 " --> pdb=" O THR C 215 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 108 through 115 Processing sheet with id=AB1, first strand: chain 'C' and resid 164 through 166 removed outlier: 3.567A pdb=" N ARG C 171 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 14 through 15 Processing sheet with id=AB3, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.315A pdb=" N VAL D 93 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU D 138 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL D 67 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 108 through 115 Processing sheet with id=AB5, first strand: chain 'D' and resid 164 through 166 Processing sheet with id=AB6, first strand: chain 'E' and resid 14 through 16 removed outlier: 3.530A pdb=" N THR E 14 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL E 16 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL E 30 " --> pdb=" O VAL E 16 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 94 through 95 removed outlier: 6.182A pdb=" N VAL E 95 " --> pdb=" O ASP E 141 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE E 140 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA E 185 " --> pdb=" O VAL E 69 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 108 through 115 removed outlier: 3.632A pdb=" N LYS E 109 " --> pdb=" O LYS E 124 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS E 124 " --> pdb=" O LYS E 109 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL E 113 " --> pdb=" O VAL E 120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 165 through 166 removed outlier: 3.631A pdb=" N ARG E 171 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 14 through 17 removed outlier: 3.546A pdb=" N VAL F 30 " --> pdb=" O VAL F 16 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 182 through 185 Processing sheet with id=AC3, first strand: chain 'F' and resid 94 through 95 Processing sheet with id=AC4, first strand: chain 'F' and resid 110 through 111 Processing sheet with id=AC5, first strand: chain 'F' and resid 164 through 165 Processing sheet with id=AC6, first strand: chain 'G' and resid 327 through 329 removed outlier: 6.864A pdb=" N GLU G 327 " --> pdb=" O HIS G 489 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLU G 454 " --> pdb=" O THR G 415 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL G 417 " --> pdb=" O GLU G 454 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU G 456 " --> pdb=" O VAL G 417 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LEU G 419 " --> pdb=" O LEU G 456 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE G 458 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU G 421 " --> pdb=" O PHE G 458 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N THR G 460 " --> pdb=" O LEU G 421 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL G 416 " --> pdb=" O ILE G 540 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LYS G 539 " --> pdb=" O GLU G 581 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 377 through 381 removed outlier: 5.332A pdb=" N PHE G 379 " --> pdb=" O GLN G 406 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLN G 406 " --> pdb=" O PHE G 379 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR G 404 " --> pdb=" O LEU G 381 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 544 through 545 removed outlier: 3.632A pdb=" N SER G 545 " --> pdb=" O ILE G 585 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE G 587 " --> pdb=" O SER G 545 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA G 584 " --> pdb=" O VAL G 599 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE G 601 " --> pdb=" O ALA G 584 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLY G 586 " --> pdb=" O ILE G 601 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'f' and resid 43 through 46 Processing sheet with id=AD1, first strand: chain 'I' and resid 451 through 456 removed outlier: 7.465A pdb=" N THR I 415 " --> pdb=" O LYS I 452 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLU I 454 " --> pdb=" O THR I 415 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL I 417 " --> pdb=" O GLU I 454 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU I 456 " --> pdb=" O VAL I 417 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU I 419 " --> pdb=" O LEU I 456 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL I 416 " --> pdb=" O ILE I 540 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N MET I 542 " --> pdb=" O VAL I 416 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR I 418 " --> pdb=" O MET I 542 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE I 544 " --> pdb=" O THR I 418 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N VAL I 420 " --> pdb=" O ILE I 544 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N VAL I 599 " --> pdb=" O LEU I 582 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA I 584 " --> pdb=" O VAL I 599 " (cutoff:3.500A) 777 hydrogen bonds defined for protein. 2211 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.17 Time building geometry restraints manager: 2.37 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: 7259 1.34 - 1.46: 4471 1.46 - 1.58: 9768 1.58 - 1.70: 15 1.70 - 1.82: 157 Bond restraints: 21670 Sorted by residual: bond pdb=" N MET f 221 " pdb=" CA MET f 221 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.09e-02 8.42e+03 9.10e+00 bond pdb=" N ILE G 441 " pdb=" CA ILE G 441 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.14e-02 7.69e+03 7.28e+00 bond pdb=" N VAL B 306 " pdb=" CA VAL B 306 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.14e-02 7.69e+03 7.27e+00 bond pdb=" N ASP C 110 " pdb=" CA ASP C 110 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.25e-02 6.40e+03 7.15e+00 bond pdb=" N ASP f 220 " pdb=" CA ASP f 220 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.32e-02 5.74e+03 6.79e+00 ... (remaining 21665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 29002 2.28 - 4.55: 404 4.55 - 6.83: 55 6.83 - 9.10: 8 9.10 - 11.38: 3 Bond angle restraints: 29472 Sorted by residual: angle pdb=" N TYR G 562 " pdb=" CA TYR G 562 " pdb=" C TYR G 562 " ideal model delta sigma weight residual 113.18 107.85 5.33 1.33e+00 5.65e-01 1.60e+01 angle pdb=" C GLU f 223 " pdb=" N GLU f 224 " pdb=" CA GLU f 224 " ideal model delta sigma weight residual 122.17 116.00 6.17 1.54e+00 4.22e-01 1.60e+01 angle pdb=" CB GLU F 320 " pdb=" CG GLU F 320 " pdb=" CD GLU F 320 " ideal model delta sigma weight residual 112.60 119.38 -6.78 1.70e+00 3.46e-01 1.59e+01 angle pdb=" CB MET A 29 " pdb=" CG MET A 29 " pdb=" SD MET A 29 " ideal model delta sigma weight residual 112.70 124.08 -11.38 3.00e+00 1.11e-01 1.44e+01 angle pdb=" CA THR B 272 " pdb=" CB THR B 272 " pdb=" OG1 THR B 272 " ideal model delta sigma weight residual 109.60 104.05 5.55 1.50e+00 4.44e-01 1.37e+01 ... (remaining 29467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 10678 17.91 - 35.81: 1703 35.81 - 53.72: 556 53.72 - 71.63: 113 71.63 - 89.53: 46 Dihedral angle restraints: 13096 sinusoidal: 5340 harmonic: 7756 Sorted by residual: dihedral pdb=" CA HIS D 176 " pdb=" C HIS D 176 " pdb=" N PRO D 177 " pdb=" CA PRO D 177 " ideal model delta harmonic sigma weight residual -180.00 -160.74 -19.26 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA LEU A 97 " pdb=" C LEU A 97 " pdb=" N ASP A 98 " pdb=" CA ASP A 98 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA TRP G 463 " pdb=" C TRP G 463 " pdb=" N LYS G 464 " pdb=" CA LYS G 464 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 13093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2492 0.047 - 0.093: 681 0.093 - 0.140: 139 0.140 - 0.186: 10 0.186 - 0.233: 5 Chirality restraints: 3327 Sorted by residual: chirality pdb=" CA MET B 268 " pdb=" N MET B 268 " pdb=" C MET B 268 " pdb=" CB MET B 268 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA TYR F 33 " pdb=" N TYR F 33 " pdb=" C TYR F 33 " pdb=" CB TYR F 33 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA VAL B 306 " pdb=" N VAL B 306 " pdb=" C VAL B 306 " pdb=" CB VAL B 306 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.59e-01 ... (remaining 3324 not shown) Planarity restraints: 3836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 276 " -0.043 2.00e-02 2.50e+03 3.19e-02 2.54e+01 pdb=" CG TRP B 276 " 0.084 2.00e-02 2.50e+03 pdb=" CD1 TRP B 276 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 276 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 276 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 276 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 276 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 276 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 276 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 276 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 271 " -0.283 9.50e-02 1.11e+02 1.27e-01 9.90e+00 pdb=" NE ARG B 271 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG B 271 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 271 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 271 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 269 " -0.039 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO E 270 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 270 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 270 " -0.033 5.00e-02 4.00e+02 ... (remaining 3833 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 137 2.41 - 3.03: 13297 3.03 - 3.65: 33622 3.65 - 4.28: 47487 4.28 - 4.90: 77691 Nonbonded interactions: 172234 Sorted by model distance: nonbonded pdb=" O2A ATP D 401 " pdb="MG MG D 402 " model vdw 1.783 2.170 nonbonded pdb=" O3G ATP D 401 " pdb="MG MG D 402 " model vdw 1.821 2.170 nonbonded pdb=" O3G ATP C 401 " pdb="MG MG C 402 " model vdw 1.836 2.170 nonbonded pdb=" OG SER F 78 " pdb="MG MG F 402 " model vdw 1.956 2.170 nonbonded pdb=" O3B ATP D 401 " pdb="MG MG D 402 " model vdw 1.967 2.170 ... (remaining 172229 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 319) selection = (chain 'B' and (resid 9 through 188 or resid 204 through 319)) selection = (chain 'C' and (resid 9 through 188 or resid 204 through 319)) selection = (chain 'D' and (resid 9 through 188 or resid 204 through 319)) selection = (chain 'E' and (resid 9 through 188 or resid 204 through 319)) selection = (chain 'F' and (resid 9 through 188 or resid 204 through 319)) } ncs_group { reference = (chain 'G' and (resid 316 through 371 or resid 413 through 619)) selection = (chain 'I' and resid 316 through 619) } 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: 4.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.330 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 25.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 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 : 0.004 0.053 21670 Z= 0.191 Angle : 0.656 11.379 29472 Z= 0.357 Chirality : 0.043 0.233 3327 Planarity : 0.005 0.127 3836 Dihedral : 19.913 89.532 8080 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 1.03 % Allowed : 43.02 % Favored : 55.95 % 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: -1.55 (0.17), residues: 2651 helix: -0.19 (0.16), residues: 1016 sheet: -1.51 (0.30), residues: 332 loop : -1.55 (0.18), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 488 TYR 0.015 0.001 TYR A 47 PHE 0.028 0.001 PHE C 290 TRP 0.084 0.002 TRP B 276 HIS 0.012 0.001 HIS F 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 (21670) covalent geometry : angle 0.65642 / 0.36 (29472) hydrogen bonds : bond 0.19159 / 12.78 ( 777) hydrogen bonds : angle 7.32143 / 5.15 ( 2211) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 551 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 279 ASN cc_start: 0.7363 (m-40) cc_final: 0.7124 (m-40) REVERT: D 284 ASN cc_start: 0.7614 (t0) cc_final: 0.7357 (t0) REVERT: E 152 PHE cc_start: 0.7529 (OUTLIER) cc_final: 0.7249 (m-80) REVERT: F 180 ARG cc_start: 0.7753 (mmp80) cc_final: 0.7402 (mmp80) outliers start: 23 outliers final: 8 residues processed: 566 average time/residue: 0.1604 time to fit residues: 134.2442 Evaluate side-chains 555 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 546 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain G residue 440 ASP Chi-restraints excluded: chain I residue 424 SER Chi-restraints excluded: chain I residue 544 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 ASN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN C 80 HIS C 133 GLN ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 GLN E 246 ASN ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 353 ASN G 589 HIS I 518 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.156161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.130914 restraints weight = 35132.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.135506 restraints weight = 18229.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.138643 restraints weight = 11364.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.140690 restraints weight = 7955.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.141990 restraints weight = 6150.623| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 21670 Z= 0.260 Angle : 0.644 9.773 29472 Z= 0.342 Chirality : 0.045 0.171 3327 Planarity : 0.005 0.072 3836 Dihedral : 9.799 71.320 3171 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 5.53 % Allowed : 37.36 % Favored : 57.11 % 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: -1.57 (0.16), residues: 2651 helix: -0.19 (0.16), residues: 1061 sheet: -1.45 (0.31), residues: 307 loop : -1.65 (0.18), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 210 TYR 0.022 0.002 TYR B 143 PHE 0.016 0.002 PHE G 321 TRP 0.044 0.002 TRP B 276 HIS 0.011 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.26 (21670) covalent geometry : angle 0.64385 / 0.34 (29472) hydrogen bonds : bond 0.05079 / 3.41 ( 777) hydrogen bonds : angle 5.86411 / 4.09 ( 2211) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 584 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 HIS cc_start: 0.6435 (OUTLIER) cc_final: 0.6015 (m90) REVERT: A 150 VAL cc_start: 0.5868 (OUTLIER) cc_final: 0.5535 (p) REVERT: A 225 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7304 (mt-10) REVERT: A 257 GLN cc_start: 0.7951 (tp-100) cc_final: 0.7544 (tp-100) REVERT: B 123 PHE cc_start: 0.8364 (p90) cc_final: 0.8048 (p90) REVERT: B 151 MET cc_start: 0.7758 (ppp) cc_final: 0.7474 (ppp) REVERT: B 210 ARG cc_start: 0.7124 (mtp180) cc_final: 0.6860 (mtp180) REVERT: B 250 ARG cc_start: 0.7122 (mmp-170) cc_final: 0.6792 (mmp-170) REVERT: B 268 MET cc_start: 0.6748 (OUTLIER) cc_final: 0.6429 (mmm) REVERT: C 110 ASP cc_start: 0.7073 (p0) cc_final: 0.6815 (p0) REVERT: C 114 VAL cc_start: 0.8611 (t) cc_final: 0.8299 (p) REVERT: C 208 MET cc_start: 0.7228 (tpp) cc_final: 0.6735 (mmm) REVERT: C 211 TRP cc_start: 0.8602 (m100) cc_final: 0.8029 (m100) REVERT: C 235 HIS cc_start: 0.6208 (OUTLIER) cc_final: 0.5886 (p-80) REVERT: C 256 ARG cc_start: 0.7485 (mtt90) cc_final: 0.7147 (mtt180) REVERT: C 276 TRP cc_start: 0.8269 (t60) cc_final: 0.7421 (t60) REVERT: D 80 HIS cc_start: 0.8055 (OUTLIER) cc_final: 0.7783 (m90) REVERT: D 125 ASP cc_start: 0.7549 (p0) cc_final: 0.6994 (p0) REVERT: D 284 ASN cc_start: 0.7450 (t0) cc_final: 0.6951 (t0) REVERT: E 19 ARG cc_start: 0.5939 (OUTLIER) cc_final: 0.5546 (mmm160) REVERT: E 89 ASN cc_start: 0.7631 (t0) cc_final: 0.7409 (t0) REVERT: F 69 VAL cc_start: 0.7921 (t) cc_final: 0.7025 (p) REVERT: F 142 GLN cc_start: 0.8382 (mp10) cc_final: 0.8081 (mp10) REVERT: F 155 GLN cc_start: 0.8434 (tp40) cc_final: 0.7998 (tp40) REVERT: F 214 VAL cc_start: 0.8247 (t) cc_final: 0.7815 (p) REVERT: G 318 TYR cc_start: 0.8079 (m-80) cc_final: 0.7861 (m-10) REVERT: G 558 ASN cc_start: 0.7589 (m-40) cc_final: 0.7310 (m110) REVERT: G 615 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.5437 (tp) REVERT: f 112 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6675 (tp30) REVERT: f 197 ARG cc_start: 0.7443 (tmt170) cc_final: 0.7105 (tmt170) REVERT: f 208 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6864 (m-80) REVERT: f 215 MET cc_start: 0.6786 (mmm) cc_final: 0.6511 (mmm) REVERT: I 517 GLU cc_start: 0.5512 (mt-10) cc_final: 0.5294 (mt-10) REVERT: I 525 ILE cc_start: 0.8237 (mm) cc_final: 0.8012 (mm) REVERT: I 620 GLU cc_start: 0.4342 (tp30) cc_final: 0.3590 (tp30) outliers start: 124 outliers final: 55 residues processed: 657 average time/residue: 0.1528 time to fit residues: 149.2035 Evaluate side-chains 642 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 578 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain G residue 394 ILE Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 503 ARG Chi-restraints excluded: chain G residue 510 MET Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 526 TRP Chi-restraints excluded: chain G residue 601 ILE Chi-restraints excluded: chain G residue 614 GLN Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 57 ARG Chi-restraints excluded: chain f residue 62 ASP Chi-restraints excluded: chain f residue 86 GLN Chi-restraints excluded: chain f residue 112 GLU Chi-restraints excluded: chain f residue 147 VAL Chi-restraints excluded: chain f residue 208 PHE Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 434 VAL Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 522 GLU Chi-restraints excluded: chain I residue 563 LEU Chi-restraints excluded: chain I residue 566 HIS Chi-restraints excluded: chain I residue 607 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 198 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 181 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 95 optimal weight: 0.0970 chunk 212 optimal weight: 0.3980 chunk 31 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 ASN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN C 80 HIS C 133 GLN ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 400 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 = 0.4054 r_free = 0.4054 target = 0.159675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.134470 restraints weight = 35077.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.139209 restraints weight = 17981.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.142349 restraints weight = 11044.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.144431 restraints weight = 7701.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.145839 restraints weight = 5921.987| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21670 Z= 0.121 Angle : 0.571 8.858 29472 Z= 0.296 Chirality : 0.041 0.176 3327 Planarity : 0.004 0.058 3836 Dihedral : 9.016 81.181 3157 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 4.73 % Allowed : 38.56 % Favored : 56.71 % 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: -1.31 (0.17), residues: 2651 helix: 0.17 (0.16), residues: 1053 sheet: -1.36 (0.31), residues: 324 loop : -1.61 (0.18), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 256 TYR 0.017 0.001 TYR B 310 PHE 0.014 0.001 PHE F 152 TRP 0.040 0.001 TRP B 276 HIS 0.009 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (21670) covalent geometry : angle 0.57053 / 0.30 (29472) hydrogen bonds : bond 0.03814 / 2.59 ( 777) hydrogen bonds : angle 5.37304 / 3.74 ( 2211) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 587 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 HIS cc_start: 0.6369 (OUTLIER) cc_final: 0.5987 (m90) REVERT: A 150 VAL cc_start: 0.5539 (OUTLIER) cc_final: 0.5148 (p) REVERT: A 225 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7169 (mt-10) REVERT: A 257 GLN cc_start: 0.7905 (tp-100) cc_final: 0.7401 (tp-100) REVERT: B 100 HIS cc_start: 0.7563 (OUTLIER) cc_final: 0.6018 (t-90) REVERT: B 151 MET cc_start: 0.7821 (ppp) cc_final: 0.7603 (ppp) REVERT: B 210 ARG cc_start: 0.7060 (mtp180) cc_final: 0.6824 (mtp180) REVERT: B 250 ARG cc_start: 0.7046 (mmp-170) cc_final: 0.6695 (mmp-170) REVERT: B 268 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.6387 (mmm) REVERT: B 290 PHE cc_start: 0.7513 (t80) cc_final: 0.7147 (t80) REVERT: C 110 ASP cc_start: 0.7096 (p0) cc_final: 0.6841 (p0) REVERT: C 211 TRP cc_start: 0.8458 (m100) cc_final: 0.7669 (m100) REVERT: C 235 HIS cc_start: 0.5909 (OUTLIER) cc_final: 0.5120 (p-80) REVERT: C 276 TRP cc_start: 0.8262 (t60) cc_final: 0.7332 (t60) REVERT: C 290 PHE cc_start: 0.8242 (t80) cc_final: 0.7800 (t80) REVERT: D 80 HIS cc_start: 0.7921 (OUTLIER) cc_final: 0.7494 (m90) REVERT: D 123 PHE cc_start: 0.7900 (t80) cc_final: 0.7696 (t80) REVERT: D 144 ASP cc_start: 0.7225 (p0) cc_final: 0.6955 (p0) REVERT: D 284 ASN cc_start: 0.7445 (t0) cc_final: 0.6930 (t0) REVERT: E 19 ARG cc_start: 0.5862 (OUTLIER) cc_final: 0.5442 (mmm160) REVERT: E 149 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6853 (t70) REVERT: E 152 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.7257 (m-80) REVERT: E 208 MET cc_start: 0.7436 (mmm) cc_final: 0.7206 (mmm) REVERT: F 142 GLN cc_start: 0.8395 (mp10) cc_final: 0.7996 (mp10) REVERT: F 155 GLN cc_start: 0.8459 (tp40) cc_final: 0.7995 (tp40) REVERT: F 214 VAL cc_start: 0.8196 (t) cc_final: 0.7838 (p) REVERT: F 251 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8665 (p) REVERT: G 318 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7837 (m-10) REVERT: G 330 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6298 (pm20) REVERT: G 346 PHE cc_start: 0.6585 (t80) cc_final: 0.6315 (t80) REVERT: G 390 ARG cc_start: 0.7825 (tpp80) cc_final: 0.7582 (tpp80) REVERT: G 558 ASN cc_start: 0.7477 (m-40) cc_final: 0.7102 (m110) REVERT: G 573 GLU cc_start: 0.7164 (pp20) cc_final: 0.6818 (pp20) REVERT: G 615 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.5450 (tp) REVERT: f 112 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6684 (tp30) REVERT: f 115 ARG cc_start: 0.8138 (tmm-80) cc_final: 0.7674 (tmm-80) REVERT: f 215 MET cc_start: 0.6786 (mmm) cc_final: 0.6456 (mmm) REVERT: I 509 MET cc_start: 0.7717 (mmm) cc_final: 0.7363 (mmt) REVERT: I 517 GLU cc_start: 0.5641 (mt-10) cc_final: 0.5437 (mt-10) outliers start: 106 outliers final: 49 residues processed: 657 average time/residue: 0.1539 time to fit residues: 148.8340 Evaluate side-chains 635 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 572 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 54 THR 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 149 ASP Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain G residue 318 TYR Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 348 ASP Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 366 GLN Chi-restraints excluded: chain G residue 394 ILE Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 526 TRP Chi-restraints excluded: chain G residue 550 VAL Chi-restraints excluded: chain G residue 614 GLN Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 57 ARG Chi-restraints excluded: chain f residue 62 ASP Chi-restraints excluded: chain f residue 86 GLN Chi-restraints excluded: chain f residue 112 GLU Chi-restraints excluded: chain f residue 179 VAL Chi-restraints excluded: chain f residue 211 THR Chi-restraints excluded: chain I residue 353 ASN Chi-restraints excluded: chain I residue 368 ARG Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain I residue 493 LYS Chi-restraints excluded: chain I residue 563 LEU Chi-restraints excluded: chain I residue 566 HIS Chi-restraints excluded: chain I residue 607 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 170 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 144 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN C 80 HIS C 83 GLN C 133 GLN C 207 GLN F 10 ASN ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 ASN ** G 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.157768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.132744 restraints weight = 35413.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137345 restraints weight = 18154.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.140381 restraints weight = 11201.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.142436 restraints weight = 7877.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.143713 restraints weight = 6054.081| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21670 Z= 0.159 Angle : 0.577 8.512 29472 Z= 0.301 Chirality : 0.042 0.172 3327 Planarity : 0.005 0.059 3836 Dihedral : 8.794 81.143 3157 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 5.26 % Allowed : 38.16 % Favored : 56.58 % 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: -1.31 (0.17), residues: 2651 helix: 0.12 (0.16), residues: 1067 sheet: -1.21 (0.31), residues: 318 loop : -1.62 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 65 TYR 0.020 0.001 TYR B 310 PHE 0.028 0.001 PHE D 179 TRP 0.035 0.002 TRP B 276 HIS 0.011 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (21670) covalent geometry : angle 0.57672 / 0.30 (29472) hydrogen bonds : bond 0.03874 / 2.62 ( 777) hydrogen bonds : angle 5.28386 / 3.67 ( 2211) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 599 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 HIS cc_start: 0.6359 (OUTLIER) cc_final: 0.5960 (m90) REVERT: A 225 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7240 (mt-10) REVERT: A 257 GLN cc_start: 0.7908 (tp-100) cc_final: 0.7385 (tp-100) REVERT: B 51 ARG cc_start: 0.7521 (ttt90) cc_final: 0.7267 (ttp80) REVERT: B 65 ARG cc_start: 0.8171 (mmm-85) cc_final: 0.7649 (mmm-85) REVERT: B 100 HIS cc_start: 0.7573 (OUTLIER) cc_final: 0.5951 (t-90) REVERT: B 151 MET cc_start: 0.7745 (ppp) cc_final: 0.7264 (ppp) REVERT: B 250 ARG cc_start: 0.7126 (mmp-170) cc_final: 0.6748 (mmp-170) REVERT: B 290 PHE cc_start: 0.7675 (t80) cc_final: 0.7364 (t80) REVERT: C 110 ASP cc_start: 0.7163 (p0) cc_final: 0.6869 (p0) REVERT: C 211 TRP cc_start: 0.8495 (m100) cc_final: 0.8230 (m100) REVERT: C 235 HIS cc_start: 0.6047 (OUTLIER) cc_final: 0.5342 (p-80) REVERT: C 276 TRP cc_start: 0.8305 (t60) cc_final: 0.7456 (t60) REVERT: C 279 ASN cc_start: 0.7403 (m-40) cc_final: 0.7020 (m-40) REVERT: C 290 PHE cc_start: 0.8304 (t80) cc_final: 0.7852 (t80) REVERT: D 80 HIS cc_start: 0.8006 (OUTLIER) cc_final: 0.7686 (m90) REVERT: E 19 ARG cc_start: 0.5881 (OUTLIER) cc_final: 0.5423 (mmm160) REVERT: E 82 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6761 (tp30) REVERT: E 149 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.6846 (t70) REVERT: E 152 PHE cc_start: 0.7587 (OUTLIER) cc_final: 0.7282 (m-80) REVERT: E 208 MET cc_start: 0.7453 (mmm) cc_final: 0.7142 (tmm) REVERT: E 209 ASP cc_start: 0.6903 (t0) cc_final: 0.6631 (t70) REVERT: F 142 GLN cc_start: 0.8373 (mp10) cc_final: 0.7971 (mp10) REVERT: F 155 GLN cc_start: 0.8481 (tp40) cc_final: 0.7971 (tp40) REVERT: F 209 ASP cc_start: 0.6853 (m-30) cc_final: 0.6385 (m-30) REVERT: F 214 VAL cc_start: 0.8175 (t) cc_final: 0.7777 (p) REVERT: F 251 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8680 (p) REVERT: G 346 PHE cc_start: 0.6712 (t80) cc_final: 0.6403 (t80) REVERT: G 500 ARG cc_start: 0.7433 (ttp80) cc_final: 0.7129 (ttp80) REVERT: G 558 ASN cc_start: 0.7488 (m-40) cc_final: 0.7109 (m110) REVERT: G 573 GLU cc_start: 0.7229 (pp20) cc_final: 0.6889 (pp20) REVERT: G 596 GLN cc_start: 0.6644 (mm-40) cc_final: 0.6375 (mm-40) REVERT: G 615 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.5255 (tp) REVERT: f 112 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6638 (tp30) REVERT: f 115 ARG cc_start: 0.8156 (tmm-80) cc_final: 0.7733 (tmm-80) REVERT: f 197 ARG cc_start: 0.7302 (tmt170) cc_final: 0.7043 (tmt170) REVERT: f 208 PHE cc_start: 0.7115 (OUTLIER) cc_final: 0.6830 (m-80) REVERT: f 215 MET cc_start: 0.6880 (mmm) cc_final: 0.6530 (mmm) REVERT: f 224 GLU cc_start: 0.5111 (OUTLIER) cc_final: 0.4843 (tm-30) REVERT: I 346 PHE cc_start: 0.7771 (m-10) cc_final: 0.7394 (m-80) REVERT: I 493 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7252 (tmtt) REVERT: I 509 MET cc_start: 0.7759 (mmm) cc_final: 0.7409 (mmt) REVERT: I 517 GLU cc_start: 0.5756 (mt-10) cc_final: 0.5414 (mt-10) REVERT: I 538 ARG cc_start: 0.6059 (mmm160) cc_final: 0.5763 (mmm160) REVERT: I 573 GLU cc_start: 0.7962 (mp0) cc_final: 0.7082 (mp0) outliers start: 118 outliers final: 66 residues processed: 674 average time/residue: 0.1610 time to fit residues: 161.2251 Evaluate side-chains 672 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 592 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 54 THR 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 82 GLU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain G residue 348 ASP Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 366 GLN Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 440 ASP Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 510 MET Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 526 TRP Chi-restraints excluded: chain G residue 550 VAL Chi-restraints excluded: chain G residue 583 ILE Chi-restraints excluded: chain G residue 601 ILE Chi-restraints excluded: chain G residue 614 GLN Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 57 ARG Chi-restraints excluded: chain f residue 62 ASP Chi-restraints excluded: chain f residue 86 GLN Chi-restraints excluded: chain f residue 112 GLU Chi-restraints excluded: chain f residue 147 VAL Chi-restraints excluded: chain f residue 180 LEU Chi-restraints excluded: chain f residue 208 PHE Chi-restraints excluded: chain f residue 211 THR Chi-restraints excluded: chain f residue 224 GLU Chi-restraints excluded: chain I residue 434 VAL Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain I residue 493 LYS Chi-restraints excluded: chain I residue 522 GLU Chi-restraints excluded: chain I residue 532 LEU Chi-restraints excluded: chain I residue 544 ILE Chi-restraints excluded: chain I residue 563 LEU Chi-restraints excluded: chain I residue 607 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 145 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 216 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 192 optimal weight: 0.9990 chunk 138 optimal weight: 0.0870 chunk 88 optimal weight: 6.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 ASN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN C 80 HIS C 83 GLN C 133 GLN C 207 GLN D 257 GLN ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.158961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.134033 restraints weight = 35206.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.138683 restraints weight = 18139.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.141766 restraints weight = 11147.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.143782 restraints weight = 7776.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.144965 restraints weight = 6001.322| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 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 : 0.003 0.048 21670 Z= 0.135 Angle : 0.573 10.143 29472 Z= 0.297 Chirality : 0.042 0.168 3327 Planarity : 0.004 0.065 3836 Dihedral : 8.614 84.889 3154 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 5.31 % Allowed : 38.43 % Favored : 56.26 % 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: -1.24 (0.17), residues: 2651 helix: 0.24 (0.16), residues: 1064 sheet: -1.19 (0.31), residues: 319 loop : -1.64 (0.18), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 210 TYR 0.022 0.001 TYR D 219 PHE 0.021 0.001 PHE D 179 TRP 0.032 0.001 TRP B 276 HIS 0.009 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (21670) covalent geometry : angle 0.57270 / 0.30 (29472) hydrogen bonds : bond 0.03598 / 2.43 ( 777) hydrogen bonds : angle 5.15183 / 3.58 ( 2211) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 588 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 HIS cc_start: 0.6346 (OUTLIER) cc_final: 0.5967 (m90) REVERT: A 225 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7225 (mt-10) REVERT: A 257 GLN cc_start: 0.7842 (tp-100) cc_final: 0.7332 (tp-100) REVERT: B 100 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.6010 (t-90) REVERT: B 151 MET cc_start: 0.7720 (ppp) cc_final: 0.7229 (ppp) REVERT: B 250 ARG cc_start: 0.7143 (mmp-170) cc_final: 0.6741 (mmp-170) REVERT: B 268 MET cc_start: 0.6614 (OUTLIER) cc_final: 0.6027 (mmm) REVERT: B 290 PHE cc_start: 0.7710 (t80) cc_final: 0.7362 (t80) REVERT: C 110 ASP cc_start: 0.7167 (p0) cc_final: 0.6873 (p0) REVERT: C 211 TRP cc_start: 0.8438 (m100) cc_final: 0.8181 (m100) REVERT: C 217 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7606 (mt) REVERT: C 235 HIS cc_start: 0.5967 (OUTLIER) cc_final: 0.4889 (p-80) REVERT: C 276 TRP cc_start: 0.8297 (t60) cc_final: 0.7534 (t60) REVERT: C 290 PHE cc_start: 0.8268 (t80) cc_final: 0.7886 (t80) REVERT: D 80 HIS cc_start: 0.7976 (OUTLIER) cc_final: 0.7566 (m90) REVERT: D 98 ASP cc_start: 0.7658 (p0) cc_final: 0.7450 (p0) REVERT: D 123 PHE cc_start: 0.7929 (t80) cc_final: 0.7714 (t80) REVERT: E 19 ARG cc_start: 0.5875 (OUTLIER) cc_final: 0.5439 (mmm160) REVERT: E 82 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6727 (tp30) REVERT: E 149 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.6834 (t70) REVERT: E 152 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.7272 (m-80) REVERT: E 209 ASP cc_start: 0.6966 (t0) cc_final: 0.6717 (t70) REVERT: F 142 GLN cc_start: 0.8394 (mp10) cc_final: 0.7907 (mp10) REVERT: F 155 GLN cc_start: 0.8479 (tp40) cc_final: 0.7943 (tp40) REVERT: F 163 ARG cc_start: 0.5130 (OUTLIER) cc_final: 0.4912 (ttm110) REVERT: F 214 VAL cc_start: 0.8166 (t) cc_final: 0.7792 (p) REVERT: G 330 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.6298 (pm20) REVERT: G 341 ASP cc_start: 0.7888 (m-30) cc_final: 0.7611 (m-30) REVERT: G 346 PHE cc_start: 0.6704 (t80) cc_final: 0.6395 (t80) REVERT: G 546 ASP cc_start: 0.7355 (OUTLIER) cc_final: 0.7075 (m-30) REVERT: G 573 GLU cc_start: 0.7244 (pp20) cc_final: 0.6967 (pp20) REVERT: G 596 GLN cc_start: 0.6651 (mm-40) cc_final: 0.6379 (mm-40) REVERT: f 112 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6624 (tp30) REVERT: f 115 ARG cc_start: 0.8131 (tmm-80) cc_final: 0.7725 (tmm-80) REVERT: f 197 ARG cc_start: 0.7345 (tmt170) cc_final: 0.7055 (tmt170) REVERT: f 208 PHE cc_start: 0.7088 (OUTLIER) cc_final: 0.6853 (m-80) REVERT: f 215 MET cc_start: 0.6890 (mmm) cc_final: 0.6502 (mmm) REVERT: I 339 GLU cc_start: 0.7679 (pp20) cc_final: 0.7018 (pt0) REVERT: I 346 PHE cc_start: 0.7765 (m-10) cc_final: 0.7382 (m-80) REVERT: I 368 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7052 (tpm170) REVERT: I 428 ARG cc_start: 0.7612 (mtp-110) cc_final: 0.7143 (mtp85) REVERT: I 448 ARG cc_start: 0.6296 (tmt170) cc_final: 0.6007 (ptm160) REVERT: I 493 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7211 (tmtt) REVERT: I 509 MET cc_start: 0.7748 (mmm) cc_final: 0.7393 (mmt) REVERT: I 517 GLU cc_start: 0.5759 (mt-10) cc_final: 0.5421 (mt-10) REVERT: I 538 ARG cc_start: 0.6077 (mmm160) cc_final: 0.5745 (mmm160) REVERT: I 574 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7529 (tp) REVERT: I 620 GLU cc_start: 0.4201 (tp30) cc_final: 0.3263 (tp30) outliers start: 119 outliers final: 70 residues processed: 663 average time/residue: 0.1584 time to fit residues: 155.2936 Evaluate side-chains 666 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 578 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 TRP Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 54 THR 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 82 GLU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 348 ASP Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 366 GLN Chi-restraints excluded: chain G residue 394 ILE Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 440 ASP Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 526 TRP Chi-restraints excluded: chain G residue 546 ASP Chi-restraints excluded: chain G residue 550 VAL Chi-restraints excluded: chain G residue 583 ILE Chi-restraints excluded: chain G residue 601 ILE Chi-restraints excluded: chain G residue 614 GLN Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 57 ARG Chi-restraints excluded: chain f residue 62 ASP Chi-restraints excluded: chain f residue 86 GLN Chi-restraints excluded: chain f residue 112 GLU Chi-restraints excluded: chain f residue 179 VAL Chi-restraints excluded: chain f residue 208 PHE Chi-restraints excluded: chain f residue 211 THR Chi-restraints excluded: chain I residue 353 ASN Chi-restraints excluded: chain I residue 368 ARG Chi-restraints excluded: chain I residue 434 VAL Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain I residue 493 LYS Chi-restraints excluded: chain I residue 522 GLU Chi-restraints excluded: chain I residue 544 ILE Chi-restraints excluded: chain I residue 563 LEU Chi-restraints excluded: chain I residue 574 ILE Chi-restraints excluded: chain I residue 607 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 98 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 chunk 221 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 217 optimal weight: 0.0170 chunk 26 optimal weight: 0.7980 chunk 209 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 ASN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS C 83 GLN C 133 GLN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 423 ASN ** 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 = 0.4032 r_free = 0.4032 target = 0.157868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.132899 restraints weight = 35200.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.137581 restraints weight = 18120.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.140612 restraints weight = 11111.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.142549 restraints weight = 7780.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.143998 restraints weight = 6035.284| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21670 Z= 0.148 Angle : 0.587 9.593 29472 Z= 0.303 Chirality : 0.042 0.163 3327 Planarity : 0.004 0.067 3836 Dihedral : 8.512 84.784 3154 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 5.66 % Allowed : 38.21 % Favored : 56.13 % 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: -1.23 (0.17), residues: 2651 helix: 0.23 (0.16), residues: 1065 sheet: -1.21 (0.31), residues: 309 loop : -1.61 (0.18), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 163 TYR 0.021 0.001 TYR A 63 PHE 0.030 0.001 PHE D 179 TRP 0.031 0.001 TRP B 276 HIS 0.010 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (21670) covalent geometry : angle 0.58707 / 0.30 (29472) hydrogen bonds : bond 0.03692 / 2.49 ( 777) hydrogen bonds : angle 5.11836 / 3.56 ( 2211) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 587 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.4167 (mmm) cc_final: 0.3758 (mmm) REVERT: A 134 HIS cc_start: 0.6344 (OUTLIER) cc_final: 0.5963 (m90) REVERT: A 225 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7207 (mt-10) REVERT: A 257 GLN cc_start: 0.7832 (tp-100) cc_final: 0.7350 (tp-100) REVERT: B 51 ARG cc_start: 0.7516 (ttt90) cc_final: 0.7235 (ttp80) REVERT: B 65 ARG cc_start: 0.8186 (mmm-85) cc_final: 0.7923 (mmm-85) REVERT: B 100 HIS cc_start: 0.7566 (OUTLIER) cc_final: 0.5955 (t-90) REVERT: B 151 MET cc_start: 0.7703 (ppp) cc_final: 0.7161 (ppp) REVERT: B 250 ARG cc_start: 0.7150 (mmp-170) cc_final: 0.6734 (mmp-170) REVERT: B 268 MET cc_start: 0.6655 (OUTLIER) cc_final: 0.6123 (mmm) REVERT: B 290 PHE cc_start: 0.7757 (t80) cc_final: 0.7363 (t80) REVERT: C 110 ASP cc_start: 0.7166 (p0) cc_final: 0.6841 (p0) REVERT: C 211 TRP cc_start: 0.8459 (m100) cc_final: 0.8185 (m100) REVERT: C 217 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7620 (mt) REVERT: C 235 HIS cc_start: 0.5940 (OUTLIER) cc_final: 0.4824 (p-80) REVERT: C 276 TRP cc_start: 0.8292 (t60) cc_final: 0.7481 (t60) REVERT: C 278 GLU cc_start: 0.6803 (pp20) cc_final: 0.6462 (pp20) REVERT: C 290 PHE cc_start: 0.8258 (t80) cc_final: 0.7881 (t80) REVERT: D 80 HIS cc_start: 0.7986 (OUTLIER) cc_final: 0.7647 (m90) REVERT: D 98 ASP cc_start: 0.7674 (p0) cc_final: 0.7471 (p0) REVERT: E 19 ARG cc_start: 0.5903 (OUTLIER) cc_final: 0.5498 (mmm160) REVERT: E 82 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6734 (tp30) REVERT: E 149 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.6906 (t70) REVERT: E 209 ASP cc_start: 0.6972 (t0) cc_final: 0.6708 (t70) REVERT: F 142 GLN cc_start: 0.8385 (mp10) cc_final: 0.7895 (mp10) REVERT: F 149 ASP cc_start: 0.7427 (p0) cc_final: 0.6988 (p0) REVERT: F 155 GLN cc_start: 0.8503 (tp40) cc_final: 0.7941 (tp40) REVERT: F 163 ARG cc_start: 0.5122 (OUTLIER) cc_final: 0.4901 (ttm110) REVERT: F 209 ASP cc_start: 0.6820 (m-30) cc_final: 0.6368 (m-30) REVERT: F 214 VAL cc_start: 0.8164 (t) cc_final: 0.7763 (p) REVERT: G 330 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6333 (pm20) REVERT: G 341 ASP cc_start: 0.7903 (m-30) cc_final: 0.7552 (m-30) REVERT: G 346 PHE cc_start: 0.6665 (t80) cc_final: 0.6349 (t80) REVERT: G 430 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.7058 (ptm-80) REVERT: G 500 ARG cc_start: 0.7335 (ttp80) cc_final: 0.6799 (ttp80) REVERT: G 546 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.7093 (m-30) REVERT: G 596 GLN cc_start: 0.6651 (mm-40) cc_final: 0.6332 (mm-40) REVERT: G 615 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.5281 (tp) REVERT: f 197 ARG cc_start: 0.7335 (tmt170) cc_final: 0.7108 (tmt170) REVERT: f 208 PHE cc_start: 0.7089 (OUTLIER) cc_final: 0.6855 (m-80) REVERT: f 215 MET cc_start: 0.6878 (mmm) cc_final: 0.6489 (mmm) REVERT: f 224 GLU cc_start: 0.5146 (OUTLIER) cc_final: 0.4824 (tm-30) REVERT: I 339 GLU cc_start: 0.7643 (pp20) cc_final: 0.7021 (pt0) REVERT: I 368 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7006 (tpm170) REVERT: I 488 ARG cc_start: 0.8237 (mmt-90) cc_final: 0.7676 (mmt-90) REVERT: I 493 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7226 (tmtt) REVERT: I 509 MET cc_start: 0.7741 (mmm) cc_final: 0.7389 (mmt) REVERT: I 517 GLU cc_start: 0.5766 (mt-10) cc_final: 0.5424 (mt-10) REVERT: I 538 ARG cc_start: 0.6060 (mmm160) cc_final: 0.5743 (mmm160) REVERT: I 542 MET cc_start: 0.6487 (tpp) cc_final: 0.6173 (tpp) REVERT: I 620 GLU cc_start: 0.4099 (tp30) cc_final: 0.3165 (tp30) outliers start: 127 outliers final: 74 residues processed: 667 average time/residue: 0.1515 time to fit residues: 150.0133 Evaluate side-chains 675 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 583 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 TRP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 54 THR 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 82 GLU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 348 ASP Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 366 GLN Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 430 ARG Chi-restraints excluded: chain G residue 440 ASP Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 510 MET Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 526 TRP Chi-restraints excluded: chain G residue 546 ASP Chi-restraints excluded: chain G residue 550 VAL Chi-restraints excluded: chain G residue 583 ILE Chi-restraints excluded: chain G residue 601 ILE Chi-restraints excluded: chain G residue 614 GLN Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 57 ARG Chi-restraints excluded: chain f residue 62 ASP Chi-restraints excluded: chain f residue 86 GLN Chi-restraints excluded: chain f residue 147 VAL Chi-restraints excluded: chain f residue 179 VAL Chi-restraints excluded: chain f residue 180 LEU Chi-restraints excluded: chain f residue 208 PHE Chi-restraints excluded: chain f residue 211 THR Chi-restraints excluded: chain f residue 224 GLU Chi-restraints excluded: chain I residue 353 ASN Chi-restraints excluded: chain I residue 368 ARG Chi-restraints excluded: chain I residue 434 VAL Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain I residue 493 LYS Chi-restraints excluded: chain I residue 532 LEU Chi-restraints excluded: chain I residue 544 ILE Chi-restraints excluded: chain I residue 607 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 52 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 64 optimal weight: 0.0770 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 ASN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 296 ASN C 80 HIS C 83 GLN C 133 GLN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 518 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.154909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.129893 restraints weight = 35496.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.134505 restraints weight = 18287.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.137572 restraints weight = 11271.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.139631 restraints weight = 7885.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141011 restraints weight = 6068.760| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 21670 Z= 0.253 Angle : 0.653 11.556 29472 Z= 0.343 Chirality : 0.045 0.167 3327 Planarity : 0.005 0.069 3836 Dihedral : 8.874 79.172 3154 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 6.38 % Allowed : 37.72 % Favored : 55.91 % 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: -1.45 (0.16), residues: 2651 helix: 0.00 (0.16), residues: 1066 sheet: -1.21 (0.31), residues: 316 loop : -1.74 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 210 TYR 0.026 0.002 TYR B 143 PHE 0.027 0.002 PHE D 179 TRP 0.037 0.002 TRP B 276 HIS 0.009 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.25 (21670) covalent geometry : angle 0.65282 / 0.34 (29472) hydrogen bonds : bond 0.04539 / 3.05 ( 777) hydrogen bonds : angle 5.36543 / 3.72 ( 2211) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 595 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7554 (tpp-160) REVERT: A 28 MET cc_start: 0.4438 (mmm) cc_final: 0.4028 (mmm) REVERT: A 134 HIS cc_start: 0.6376 (OUTLIER) cc_final: 0.5973 (m90) REVERT: A 225 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7256 (mt-10) REVERT: A 257 GLN cc_start: 0.7861 (tp-100) cc_final: 0.7390 (tp-100) REVERT: B 100 HIS cc_start: 0.7729 (OUTLIER) cc_final: 0.6038 (t-90) REVERT: B 151 MET cc_start: 0.7675 (ppp) cc_final: 0.6921 (ppp) REVERT: B 210 ARG cc_start: 0.7252 (mtp180) cc_final: 0.6912 (mtp180) REVERT: B 250 ARG cc_start: 0.7262 (mmp-170) cc_final: 0.6834 (mmp-170) REVERT: B 268 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.6134 (mmm) REVERT: B 290 PHE cc_start: 0.7866 (t80) cc_final: 0.7409 (t80) REVERT: C 80 HIS cc_start: 0.7188 (m90) cc_final: 0.6642 (m-70) REVERT: C 87 ARG cc_start: 0.8810 (mmt90) cc_final: 0.8593 (mmt90) REVERT: C 110 ASP cc_start: 0.7199 (p0) cc_final: 0.6875 (p0) REVERT: C 114 VAL cc_start: 0.8578 (t) cc_final: 0.8241 (p) REVERT: C 211 TRP cc_start: 0.8507 (m100) cc_final: 0.8275 (m100) REVERT: C 217 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7682 (mt) REVERT: C 235 HIS cc_start: 0.6104 (OUTLIER) cc_final: 0.5545 (p-80) REVERT: C 248 MET cc_start: 0.6724 (ptm) cc_final: 0.6371 (ptm) REVERT: C 276 TRP cc_start: 0.8279 (t60) cc_final: 0.7416 (t60) REVERT: C 290 PHE cc_start: 0.8322 (t80) cc_final: 0.7896 (t80) REVERT: D 80 HIS cc_start: 0.8081 (OUTLIER) cc_final: 0.7851 (m90) REVERT: D 151 MET cc_start: 0.7709 (mmm) cc_final: 0.7257 (mmm) REVERT: D 253 ASP cc_start: 0.7229 (t0) cc_final: 0.7002 (t0) REVERT: E 19 ARG cc_start: 0.6020 (OUTLIER) cc_final: 0.5636 (mmm160) REVERT: E 82 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6814 (tp30) REVERT: E 89 ASN cc_start: 0.7633 (t0) cc_final: 0.7388 (t0) REVERT: E 149 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.6826 (t70) REVERT: E 152 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.7349 (m-80) REVERT: F 142 GLN cc_start: 0.8360 (mp10) cc_final: 0.7862 (mp10) REVERT: F 163 ARG cc_start: 0.5137 (OUTLIER) cc_final: 0.4928 (ttm110) REVERT: F 209 ASP cc_start: 0.6938 (m-30) cc_final: 0.6444 (m-30) REVERT: F 214 VAL cc_start: 0.8232 (t) cc_final: 0.7804 (p) REVERT: G 341 ASP cc_start: 0.7955 (m-30) cc_final: 0.7597 (m-30) REVERT: G 346 PHE cc_start: 0.6650 (t80) cc_final: 0.6345 (t80) REVERT: G 427 MET cc_start: 0.6136 (tpp) cc_final: 0.5918 (tpp) REVERT: G 430 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.7098 (ptm-80) REVERT: G 500 ARG cc_start: 0.7370 (ttp80) cc_final: 0.6868 (ttp80) REVERT: G 596 GLN cc_start: 0.6745 (mm-40) cc_final: 0.6438 (mm-40) REVERT: f 197 ARG cc_start: 0.7375 (tmt170) cc_final: 0.7151 (tmt170) REVERT: f 208 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.6881 (m-80) REVERT: f 215 MET cc_start: 0.6895 (mmm) cc_final: 0.6551 (mmm) REVERT: f 224 GLU cc_start: 0.5066 (OUTLIER) cc_final: 0.4742 (tm-30) REVERT: I 334 LEU cc_start: 0.6803 (tp) cc_final: 0.6572 (tt) REVERT: I 346 PHE cc_start: 0.7906 (m-10) cc_final: 0.7568 (m-80) REVERT: I 368 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.6953 (tpm170) REVERT: I 493 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7171 (tmtt) REVERT: I 509 MET cc_start: 0.7789 (mmm) cc_final: 0.7432 (mmt) REVERT: I 517 GLU cc_start: 0.5736 (mt-10) cc_final: 0.5356 (mt-10) REVERT: I 538 ARG cc_start: 0.6164 (mmm160) cc_final: 0.5831 (mmm160) REVERT: I 542 MET cc_start: 0.6526 (tpp) cc_final: 0.6195 (tpp) REVERT: I 565 ARG cc_start: 0.7931 (ptm160) cc_final: 0.7595 (ptm160) REVERT: I 574 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7593 (tp) REVERT: I 620 GLU cc_start: 0.4208 (tp30) cc_final: 0.3336 (tp30) outliers start: 143 outliers final: 92 residues processed: 695 average time/residue: 0.1445 time to fit residues: 150.6857 Evaluate side-chains 698 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 588 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 90 TRP Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 TRP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain G residue 321 PHE Chi-restraints excluded: chain G residue 348 ASP Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 366 GLN Chi-restraints excluded: chain G residue 372 GLN Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 430 ARG Chi-restraints excluded: chain G residue 440 ASP Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 510 MET Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 526 TRP Chi-restraints excluded: chain G residue 546 ASP Chi-restraints excluded: chain G residue 550 VAL Chi-restraints excluded: chain G residue 601 ILE Chi-restraints excluded: chain G residue 614 GLN Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain f residue 17 THR Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 57 ARG Chi-restraints excluded: chain f residue 62 ASP Chi-restraints excluded: chain f residue 70 HIS Chi-restraints excluded: chain f residue 86 GLN Chi-restraints excluded: chain f residue 100 GLU Chi-restraints excluded: chain f residue 147 VAL Chi-restraints excluded: chain f residue 179 VAL Chi-restraints excluded: chain f residue 208 PHE Chi-restraints excluded: chain f residue 211 THR Chi-restraints excluded: chain f residue 224 GLU Chi-restraints excluded: chain I residue 368 ARG Chi-restraints excluded: chain I residue 434 VAL Chi-restraints excluded: chain I residue 493 LYS Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 530 ARG Chi-restraints excluded: chain I residue 532 LEU Chi-restraints excluded: chain I residue 544 ILE Chi-restraints excluded: chain I residue 563 LEU Chi-restraints excluded: chain I residue 574 ILE Chi-restraints excluded: chain I residue 607 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 69 optimal weight: 0.9980 chunk 232 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 251 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 229 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 ASN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN C 133 GLN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 HIS ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 423 ASN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 518 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.157526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.132632 restraints weight = 35216.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.137177 restraints weight = 18211.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.140223 restraints weight = 11284.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.142295 restraints weight = 7916.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.143710 restraints weight = 6084.974| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21670 Z= 0.145 Angle : 0.618 11.032 29472 Z= 0.317 Chirality : 0.043 0.235 3327 Planarity : 0.005 0.069 3836 Dihedral : 8.624 87.503 3154 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 5.31 % Allowed : 39.37 % Favored : 55.33 % 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: -1.32 (0.17), residues: 2651 helix: 0.13 (0.16), residues: 1069 sheet: -1.09 (0.32), residues: 313 loop : -1.69 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 312 TYR 0.020 0.001 TYR G 595 PHE 0.024 0.001 PHE D 179 TRP 0.047 0.002 TRP B 276 HIS 0.005 0.001 HIS G 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (21670) covalent geometry : angle 0.61796 / 0.32 (29472) hydrogen bonds : bond 0.03761 / 2.54 ( 777) hydrogen bonds : angle 5.15891 / 3.58 ( 2211) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 560 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7546 (tpp-160) REVERT: A 28 MET cc_start: 0.4130 (mmm) cc_final: 0.3769 (mmm) REVERT: A 134 HIS cc_start: 0.6336 (OUTLIER) cc_final: 0.5916 (m90) REVERT: A 225 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7164 (mt-10) REVERT: A 257 GLN cc_start: 0.7764 (tp-100) cc_final: 0.7334 (tp-100) REVERT: B 100 HIS cc_start: 0.7593 (OUTLIER) cc_final: 0.5940 (t-90) REVERT: B 151 MET cc_start: 0.7677 (ppp) cc_final: 0.7334 (ppp) REVERT: B 210 ARG cc_start: 0.7191 (mtp180) cc_final: 0.6965 (mtp180) REVERT: B 250 ARG cc_start: 0.7210 (mmp-170) cc_final: 0.6757 (mmp-170) REVERT: B 268 MET cc_start: 0.6761 (OUTLIER) cc_final: 0.6069 (mmm) REVERT: B 290 PHE cc_start: 0.7797 (t80) cc_final: 0.7374 (t80) REVERT: C 110 ASP cc_start: 0.7163 (p0) cc_final: 0.6815 (p0) REVERT: C 211 TRP cc_start: 0.8401 (m100) cc_final: 0.8087 (m100) REVERT: C 217 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7331 (mt) REVERT: C 235 HIS cc_start: 0.5925 (OUTLIER) cc_final: 0.4780 (p-80) REVERT: C 248 MET cc_start: 0.6720 (ptm) cc_final: 0.6354 (ptm) REVERT: C 276 TRP cc_start: 0.8265 (t60) cc_final: 0.7511 (t60) REVERT: D 80 HIS cc_start: 0.7962 (OUTLIER) cc_final: 0.7598 (m90) REVERT: D 151 MET cc_start: 0.7625 (mmm) cc_final: 0.7138 (mmm) REVERT: D 248 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6710 (tpp) REVERT: D 253 ASP cc_start: 0.7157 (t0) cc_final: 0.6926 (t0) REVERT: E 19 ARG cc_start: 0.5963 (OUTLIER) cc_final: 0.5654 (mmm160) REVERT: E 82 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6757 (tp30) REVERT: E 89 ASN cc_start: 0.7659 (t0) cc_final: 0.7361 (t0) REVERT: E 149 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.6831 (t70) REVERT: E 152 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.7327 (m-80) REVERT: E 210 ARG cc_start: 0.8095 (mtt-85) cc_final: 0.7827 (mtt180) REVERT: F 142 GLN cc_start: 0.8325 (mp10) cc_final: 0.7802 (mp10) REVERT: F 155 GLN cc_start: 0.8467 (tp40) cc_final: 0.7958 (tp40) REVERT: F 163 ARG cc_start: 0.5111 (OUTLIER) cc_final: 0.4901 (ttm110) REVERT: F 209 ASP cc_start: 0.6767 (m-30) cc_final: 0.6310 (m-30) REVERT: F 214 VAL cc_start: 0.8184 (t) cc_final: 0.7796 (p) REVERT: F 224 ASN cc_start: 0.7972 (m110) cc_final: 0.7758 (m110) REVERT: F 296 ASN cc_start: 0.8711 (m110) cc_final: 0.8246 (m110) REVERT: G 318 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.7782 (m-10) REVERT: G 330 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6292 (pm20) REVERT: G 341 ASP cc_start: 0.7889 (m-30) cc_final: 0.7496 (m-30) REVERT: G 346 PHE cc_start: 0.6605 (t80) cc_final: 0.6284 (t80) REVERT: G 427 MET cc_start: 0.6003 (tpp) cc_final: 0.5801 (tpp) REVERT: G 430 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7069 (ptm-80) REVERT: G 558 ASN cc_start: 0.7524 (m-40) cc_final: 0.7177 (m110) REVERT: G 593 ARG cc_start: 0.6675 (ptm160) cc_final: 0.6307 (ptt180) REVERT: G 596 GLN cc_start: 0.6676 (mm-40) cc_final: 0.6358 (mm-40) REVERT: G 615 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.5403 (tp) REVERT: f 197 ARG cc_start: 0.7339 (tmt170) cc_final: 0.7108 (tmt170) REVERT: f 208 PHE cc_start: 0.7114 (OUTLIER) cc_final: 0.6871 (m-80) REVERT: f 215 MET cc_start: 0.6898 (mmm) cc_final: 0.6554 (mmm) REVERT: f 224 GLU cc_start: 0.5101 (OUTLIER) cc_final: 0.4736 (tm-30) REVERT: I 339 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7052 (pt0) REVERT: I 368 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6886 (tpm170) REVERT: I 493 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.7136 (tmtt) REVERT: I 509 MET cc_start: 0.7752 (mmm) cc_final: 0.7399 (mmt) REVERT: I 517 GLU cc_start: 0.5787 (mt-10) cc_final: 0.5382 (mt-10) REVERT: I 538 ARG cc_start: 0.6111 (mmm160) cc_final: 0.5778 (mmm160) REVERT: I 542 MET cc_start: 0.6473 (tpp) cc_final: 0.6151 (tpp) REVERT: I 565 ARG cc_start: 0.7934 (ptm160) cc_final: 0.7589 (ptm160) REVERT: I 574 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7578 (tp) REVERT: I 620 GLU cc_start: 0.4300 (tp30) cc_final: 0.3475 (tp30) outliers start: 119 outliers final: 79 residues processed: 643 average time/residue: 0.1543 time to fit residues: 148.4051 Evaluate side-chains 660 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 558 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 TRP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain G residue 318 TYR Chi-restraints excluded: chain G residue 321 PHE Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 348 ASP Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 366 GLN Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 423 ASN Chi-restraints excluded: chain G residue 430 ARG Chi-restraints excluded: chain G residue 440 ASP Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 510 MET Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 526 TRP Chi-restraints excluded: chain G residue 546 ASP Chi-restraints excluded: chain G residue 550 VAL Chi-restraints excluded: chain G residue 601 ILE Chi-restraints excluded: chain G residue 614 GLN Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 57 ARG Chi-restraints excluded: chain f residue 62 ASP Chi-restraints excluded: chain f residue 70 HIS Chi-restraints excluded: chain f residue 86 GLN Chi-restraints excluded: chain f residue 147 VAL Chi-restraints excluded: chain f residue 179 VAL Chi-restraints excluded: chain f residue 208 PHE Chi-restraints excluded: chain f residue 211 THR Chi-restraints excluded: chain f residue 224 GLU Chi-restraints excluded: chain I residue 339 GLU Chi-restraints excluded: chain I residue 353 ASN Chi-restraints excluded: chain I residue 368 ARG Chi-restraints excluded: chain I residue 434 VAL Chi-restraints excluded: chain I residue 493 LYS Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 530 ARG Chi-restraints excluded: chain I residue 532 LEU Chi-restraints excluded: chain I residue 563 LEU Chi-restraints excluded: chain I residue 574 ILE Chi-restraints excluded: chain I residue 607 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 241 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 212 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 ASN ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS C 83 GLN C 133 GLN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 423 ASN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 HIS ** 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 = 0.4029 r_free = 0.4029 target = 0.157564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.132715 restraints weight = 35227.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137287 restraints weight = 18225.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.140326 restraints weight = 11292.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.142386 restraints weight = 7916.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.143609 restraints weight = 6087.897| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21670 Z= 0.149 Angle : 0.623 12.047 29472 Z= 0.319 Chirality : 0.043 0.212 3327 Planarity : 0.005 0.071 3836 Dihedral : 8.509 88.279 3154 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 4.95 % Allowed : 39.77 % Favored : 55.28 % 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: -1.27 (0.17), residues: 2651 helix: 0.18 (0.16), residues: 1061 sheet: -1.05 (0.32), residues: 313 loop : -1.66 (0.18), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 428 TYR 0.022 0.001 TYR A 63 PHE 0.024 0.001 PHE D 179 TRP 0.048 0.002 TRP B 276 HIS 0.011 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (21670) covalent geometry : angle 0.62269 / 0.32 (29472) hydrogen bonds : bond 0.03711 / 2.51 ( 777) hydrogen bonds : angle 5.11260 / 3.54 ( 2211) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 566 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7558 (tpp-160) REVERT: A 28 MET cc_start: 0.4173 (mmm) cc_final: 0.3791 (mmm) REVERT: A 134 HIS cc_start: 0.6338 (OUTLIER) cc_final: 0.5918 (m90) REVERT: A 225 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7199 (mt-10) REVERT: A 257 GLN cc_start: 0.7750 (tp-100) cc_final: 0.7342 (tp-100) REVERT: B 51 ARG cc_start: 0.7450 (ttt90) cc_final: 0.7158 (ttp80) REVERT: B 65 ARG cc_start: 0.8217 (mmm-85) cc_final: 0.7703 (mmm-85) REVERT: B 100 HIS cc_start: 0.7583 (OUTLIER) cc_final: 0.6004 (t-90) REVERT: B 151 MET cc_start: 0.7692 (ppp) cc_final: 0.7380 (ppp) REVERT: B 210 ARG cc_start: 0.7216 (mtp180) cc_final: 0.6975 (mtp180) REVERT: B 250 ARG cc_start: 0.7188 (mmp-170) cc_final: 0.6745 (mmp-170) REVERT: B 268 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6089 (mmm) REVERT: B 290 PHE cc_start: 0.7818 (t80) cc_final: 0.7379 (t80) REVERT: C 110 ASP cc_start: 0.7151 (p0) cc_final: 0.6782 (p0) REVERT: C 211 TRP cc_start: 0.8423 (m100) cc_final: 0.8133 (m100) REVERT: C 217 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7350 (mt) REVERT: C 235 HIS cc_start: 0.5963 (OUTLIER) cc_final: 0.4800 (p-80) REVERT: C 276 TRP cc_start: 0.8261 (t60) cc_final: 0.7532 (t60) REVERT: D 80 HIS cc_start: 0.7967 (OUTLIER) cc_final: 0.7559 (m90) REVERT: D 248 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6788 (tpp) REVERT: D 253 ASP cc_start: 0.7138 (t0) cc_final: 0.6912 (t0) REVERT: E 19 ARG cc_start: 0.5938 (OUTLIER) cc_final: 0.5440 (mmm160) REVERT: E 27 ASP cc_start: 0.6974 (t0) cc_final: 0.6723 (t0) REVERT: E 82 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6793 (tp30) REVERT: E 89 ASN cc_start: 0.7659 (t0) cc_final: 0.7340 (t0) REVERT: E 149 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.6900 (t70) REVERT: E 210 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7844 (mtt180) REVERT: F 142 GLN cc_start: 0.8321 (mp10) cc_final: 0.7817 (mp10) REVERT: F 155 GLN cc_start: 0.8456 (tp40) cc_final: 0.7987 (tp40) REVERT: F 163 ARG cc_start: 0.5100 (OUTLIER) cc_final: 0.4886 (ttm110) REVERT: F 209 ASP cc_start: 0.6738 (m-30) cc_final: 0.6291 (m-30) REVERT: F 214 VAL cc_start: 0.8199 (t) cc_final: 0.7809 (p) REVERT: F 296 ASN cc_start: 0.8716 (m110) cc_final: 0.8244 (m110) REVERT: G 318 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.7746 (m-10) REVERT: G 330 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6338 (pm20) REVERT: G 346 PHE cc_start: 0.6598 (t80) cc_final: 0.6291 (t80) REVERT: G 390 ARG cc_start: 0.7807 (tpp80) cc_final: 0.7452 (tpp80) REVERT: G 430 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.7139 (ptm-80) REVERT: G 558 ASN cc_start: 0.7530 (m-40) cc_final: 0.7180 (m110) REVERT: G 593 ARG cc_start: 0.6706 (ptm160) cc_final: 0.6320 (ptt180) REVERT: G 596 GLN cc_start: 0.6697 (mm-40) cc_final: 0.6379 (mm-40) REVERT: f 108 PHE cc_start: 0.8078 (t80) cc_final: 0.7339 (t80) REVERT: f 197 ARG cc_start: 0.7368 (tmt170) cc_final: 0.7150 (tmt170) REVERT: f 208 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6908 (m-80) REVERT: f 215 MET cc_start: 0.6902 (mmm) cc_final: 0.6584 (mmm) REVERT: f 224 GLU cc_start: 0.5103 (OUTLIER) cc_final: 0.4715 (tm-30) REVERT: I 339 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7073 (pt0) REVERT: I 346 PHE cc_start: 0.7871 (m-10) cc_final: 0.7468 (m-80) REVERT: I 509 MET cc_start: 0.7723 (mmm) cc_final: 0.7398 (mmt) REVERT: I 517 GLU cc_start: 0.5804 (mt-10) cc_final: 0.5366 (mt-10) REVERT: I 538 ARG cc_start: 0.6145 (mmm160) cc_final: 0.5795 (mmm160) REVERT: I 542 MET cc_start: 0.6480 (tpp) cc_final: 0.6182 (tpp) REVERT: I 565 ARG cc_start: 0.7929 (ptm160) cc_final: 0.7588 (ptm160) REVERT: I 574 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7583 (tp) outliers start: 111 outliers final: 83 residues processed: 645 average time/residue: 0.1585 time to fit residues: 151.9804 Evaluate side-chains 666 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 564 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 TRP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain G residue 318 TYR Chi-restraints excluded: chain G residue 321 PHE Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 348 ASP Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 366 GLN Chi-restraints excluded: chain G residue 383 GLU Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 423 ASN Chi-restraints excluded: chain G residue 430 ARG Chi-restraints excluded: chain G residue 440 ASP Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 546 ASP Chi-restraints excluded: chain G residue 550 VAL Chi-restraints excluded: chain G residue 556 SER Chi-restraints excluded: chain G residue 601 ILE Chi-restraints excluded: chain G residue 614 GLN Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 57 ARG Chi-restraints excluded: chain f residue 62 ASP Chi-restraints excluded: chain f residue 70 HIS Chi-restraints excluded: chain f residue 86 GLN Chi-restraints excluded: chain f residue 100 GLU Chi-restraints excluded: chain f residue 147 VAL Chi-restraints excluded: chain f residue 179 VAL Chi-restraints excluded: chain f residue 208 PHE Chi-restraints excluded: chain f residue 211 THR Chi-restraints excluded: chain f residue 224 GLU Chi-restraints excluded: chain I residue 339 GLU Chi-restraints excluded: chain I residue 353 ASN Chi-restraints excluded: chain I residue 434 VAL Chi-restraints excluded: chain I residue 493 LYS Chi-restraints excluded: chain I residue 530 ARG Chi-restraints excluded: chain I residue 532 LEU Chi-restraints excluded: chain I residue 563 LEU Chi-restraints excluded: chain I residue 574 ILE Chi-restraints excluded: chain I residue 607 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 13 optimal weight: 3.9990 chunk 187 optimal weight: 0.0670 chunk 226 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 ASN ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN B 257 GLN C 80 HIS C 83 GLN C 133 GLN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 518 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.153525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128552 restraints weight = 35268.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.133034 restraints weight = 18371.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.136054 restraints weight = 11467.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.138115 restraints weight = 8092.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.139519 restraints weight = 6230.407| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 21670 Z= 0.303 Angle : 0.723 14.038 29472 Z= 0.378 Chirality : 0.047 0.242 3327 Planarity : 0.005 0.070 3836 Dihedral : 9.023 79.420 3154 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 4.99 % Allowed : 39.86 % Favored : 55.15 % 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: -1.60 (0.16), residues: 2651 helix: -0.14 (0.16), residues: 1069 sheet: -1.20 (0.31), residues: 305 loop : -1.81 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 501 TYR 0.033 0.002 TYR C 219 PHE 0.027 0.002 PHE D 179 TRP 0.052 0.003 TRP G 526 HIS 0.010 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.30 (21670) covalent geometry : angle 0.72314 / 0.38 (29472) hydrogen bonds : bond 0.04976 / 3.34 ( 777) hydrogen bonds : angle 5.52520 / 3.83 ( 2211) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 589 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7625 (tpp-160) REVERT: A 28 MET cc_start: 0.4445 (mmm) cc_final: 0.4033 (mmm) REVERT: A 134 HIS cc_start: 0.6392 (OUTLIER) cc_final: 0.5973 (m90) REVERT: A 225 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7212 (mt-10) REVERT: A 257 GLN cc_start: 0.7834 (tp-100) cc_final: 0.7382 (tp-100) REVERT: B 65 ARG cc_start: 0.8284 (mmm-85) cc_final: 0.7770 (mmm-85) REVERT: B 100 HIS cc_start: 0.7764 (OUTLIER) cc_final: 0.6103 (t-90) REVERT: B 123 PHE cc_start: 0.8350 (p90) cc_final: 0.8137 (p90) REVERT: B 180 ARG cc_start: 0.8013 (mmt-90) cc_final: 0.7545 (mtt90) REVERT: B 210 ARG cc_start: 0.7292 (mtp180) cc_final: 0.6896 (mtp180) REVERT: B 250 ARG cc_start: 0.7365 (mmp-170) cc_final: 0.6909 (mmp-170) REVERT: B 268 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6242 (mmm) REVERT: B 290 PHE cc_start: 0.7917 (t80) cc_final: 0.7461 (t80) REVERT: B 292 LEU cc_start: 0.7793 (tt) cc_final: 0.7564 (tp) REVERT: C 87 ARG cc_start: 0.8809 (mmt90) cc_final: 0.8569 (mmt90) REVERT: C 110 ASP cc_start: 0.7222 (p0) cc_final: 0.6873 (p0) REVERT: C 217 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7633 (mt) REVERT: C 235 HIS cc_start: 0.6144 (OUTLIER) cc_final: 0.5308 (p-80) REVERT: C 276 TRP cc_start: 0.8262 (t60) cc_final: 0.7582 (t60) REVERT: D 151 MET cc_start: 0.7793 (mmm) cc_final: 0.7264 (mmm) REVERT: D 210 ARG cc_start: 0.7734 (mtt90) cc_final: 0.7503 (mmt-90) REVERT: D 253 ASP cc_start: 0.7258 (t0) cc_final: 0.6923 (t0) REVERT: E 19 ARG cc_start: 0.5986 (OUTLIER) cc_final: 0.5539 (mmm160) REVERT: E 87 ARG cc_start: 0.8125 (mmt90) cc_final: 0.7914 (mmt90) REVERT: E 89 ASN cc_start: 0.7690 (t0) cc_final: 0.7368 (t0) REVERT: F 69 VAL cc_start: 0.8003 (t) cc_final: 0.7040 (p) REVERT: F 142 GLN cc_start: 0.8345 (mp10) cc_final: 0.7834 (mp10) REVERT: F 163 ARG cc_start: 0.5177 (OUTLIER) cc_final: 0.4951 (ttm110) REVERT: F 214 VAL cc_start: 0.8206 (t) cc_final: 0.7738 (p) REVERT: F 296 ASN cc_start: 0.8697 (m110) cc_final: 0.8243 (m110) REVERT: G 330 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6388 (pm20) REVERT: G 341 ASP cc_start: 0.7946 (m-30) cc_final: 0.7572 (m-30) REVERT: G 346 PHE cc_start: 0.6611 (t80) cc_final: 0.6317 (t80) REVERT: G 390 ARG cc_start: 0.7936 (tpp80) cc_final: 0.7683 (tpp80) REVERT: G 558 ASN cc_start: 0.7673 (m-40) cc_final: 0.7408 (m-40) REVERT: G 596 GLN cc_start: 0.6823 (mm-40) cc_final: 0.6480 (mm-40) REVERT: G 615 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.5797 (tp) REVERT: f 197 ARG cc_start: 0.7402 (tmt170) cc_final: 0.7193 (tmt170) REVERT: f 208 PHE cc_start: 0.7178 (OUTLIER) cc_final: 0.6963 (m-80) REVERT: f 215 MET cc_start: 0.6910 (mmm) cc_final: 0.6590 (mmm) REVERT: f 224 GLU cc_start: 0.5093 (OUTLIER) cc_final: 0.4688 (tm-30) REVERT: I 493 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7149 (tmtt) REVERT: I 509 MET cc_start: 0.7825 (mmm) cc_final: 0.7448 (mmp) REVERT: I 517 GLU cc_start: 0.5685 (mt-10) cc_final: 0.5274 (mt-10) REVERT: I 538 ARG cc_start: 0.6209 (mmm160) cc_final: 0.5848 (mmm160) REVERT: I 542 MET cc_start: 0.6517 (tpp) cc_final: 0.6205 (tpp) REVERT: I 565 ARG cc_start: 0.8062 (ptm160) cc_final: 0.7692 (ptm160) REVERT: I 574 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7647 (tp) outliers start: 112 outliers final: 81 residues processed: 668 average time/residue: 0.1667 time to fit residues: 165.0412 Evaluate side-chains 678 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 583 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 90 TRP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 77 LYS 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 153 VAL Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 321 PHE Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 348 ASP Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 366 GLN Chi-restraints excluded: chain G residue 383 GLU Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 440 ASP Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 510 MET Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 550 VAL Chi-restraints excluded: chain G residue 601 ILE Chi-restraints excluded: chain G residue 614 GLN Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 57 ARG Chi-restraints excluded: chain f residue 62 ASP Chi-restraints excluded: chain f residue 70 HIS Chi-restraints excluded: chain f residue 86 GLN Chi-restraints excluded: chain f residue 100 GLU Chi-restraints excluded: chain f residue 147 VAL Chi-restraints excluded: chain f residue 179 VAL Chi-restraints excluded: chain f residue 208 PHE Chi-restraints excluded: chain f residue 211 THR Chi-restraints excluded: chain f residue 224 GLU Chi-restraints excluded: chain I residue 434 VAL Chi-restraints excluded: chain I residue 493 LYS Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 530 ARG Chi-restraints excluded: chain I residue 532 LEU Chi-restraints excluded: chain I residue 563 LEU Chi-restraints excluded: chain I residue 574 ILE Chi-restraints excluded: chain I residue 607 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 213 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 232 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 141 optimal weight: 0.7980 chunk 98 optimal weight: 0.1980 chunk 258 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 ASN ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 GLN ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 489 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.157807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.132984 restraints weight = 35291.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.137547 restraints weight = 18282.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.140692 restraints weight = 11310.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.142468 restraints weight = 7847.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.143998 restraints weight = 6145.635| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21670 Z= 0.140 Angle : 0.659 15.065 29472 Z= 0.334 Chirality : 0.044 0.204 3327 Planarity : 0.005 0.070 3836 Dihedral : 8.631 89.703 3154 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 4.37 % Allowed : 40.97 % Favored : 54.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.17), residues: 2651 helix: 0.10 (0.16), residues: 1063 sheet: -1.13 (0.32), residues: 314 loop : -1.72 (0.18), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 501 TYR 0.040 0.001 TYR D 219 PHE 0.022 0.001 PHE D 179 TRP 0.067 0.002 TRP B 276 HIS 0.014 0.001 HIS F 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (21670) covalent geometry : angle 0.65896 / 0.33 (29472) hydrogen bonds : bond 0.03765 / 2.55 ( 777) hydrogen bonds : angle 5.14086 / 3.55 ( 2211) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4092.26 seconds wall clock time: 71 minutes 10.93 seconds (4270.93 seconds total)