Starting phenix.real_space_refine on Wed Sep 17 19:41:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hra_0257/09_2025/6hra_0257.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hra_0257/09_2025/6hra_0257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6hra_0257/09_2025/6hra_0257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hra_0257/09_2025/6hra_0257.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hra_0257/09_2025/6hra_0257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hra_0257/09_2025/6hra_0257.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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 K 3 8.98 5 P 1 5.49 5 S 61 5.16 5 C 6968 2.51 5 N 1823 2.21 5 O 1962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10818 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "C" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1413 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 13, 'TRANS': 173} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 5047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5047 Classifications: {'peptide': 679} Link IDs: {'PTRANS': 26, 'TRANS': 652} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.62, per 1000 atoms: 0.24 Number of scatterers: 10818 At special positions: 0 Unit cell: (98.164, 113.344, 152.812, 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) K 3 19.00 S 61 16.00 P 1 15.00 O 1962 8.00 N 1823 7.00 C 6968 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: 1.00 Conformation dependent library (CDL) restraints added in 558.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2640 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 8 sheets defined 58.2% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 2 through 32 removed outlier: 3.639A pdb=" N LEU A 7 " --> pdb=" O ALA A 3 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 8 " --> pdb=" O GLN A 4 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 9 " --> pdb=" O GLY A 5 " (cutoff:3.500A) Proline residue: A 22 - end of helix removed outlier: 3.534A pdb=" N SER A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 47 Processing helix chain 'A' and resid 58 through 70 removed outlier: 3.587A pdb=" N CYS A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 65 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 66 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 83 removed outlier: 3.738A pdb=" N VAL A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 82 " --> pdb=" O PHE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 111 removed outlier: 3.544A pdb=" N PHE A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 removed outlier: 3.692A pdb=" N ALA A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 157 removed outlier: 3.627A pdb=" N LEU A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 removed outlier: 3.874A pdb=" N ARG A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 193 removed outlier: 3.618A pdb=" N PHE A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 4.377A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.607A pdb=" N ASN A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 274 removed outlier: 4.387A pdb=" N CYS A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 304 removed outlier: 4.084A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL A 289 " --> pdb=" O TRP A 285 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.207A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 removed outlier: 3.703A pdb=" N VAL A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.590A pdb=" N PHE A 354 " --> pdb=" O HIS A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 368 removed outlier: 3.844A pdb=" N MET A 366 " --> pdb=" O PRO A 362 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A 367 " --> pdb=" O MET A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 391 removed outlier: 4.028A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.868A pdb=" N LEU A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 438 removed outlier: 3.581A pdb=" N VAL A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 429 " --> pdb=" O PRO A 425 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.803A pdb=" N ARG A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 removed outlier: 3.940A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 495 removed outlier: 3.511A pdb=" N CYS A 483 " --> pdb=" O PRO A 479 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A 486 " --> pdb=" O ASN A 482 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 492 " --> pdb=" O CYS A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 507 removed outlier: 3.875A pdb=" N ILE A 503 " --> pdb=" O PRO A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 539 removed outlier: 3.713A pdb=" N GLY A 533 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 Processing helix chain 'A' and resid 550 through 557 removed outlier: 3.715A pdb=" N SER A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 12 removed outlier: 3.573A pdb=" N PHE C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 20 removed outlier: 3.739A pdb=" N GLY C 19 " --> pdb=" O LEU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 34 removed outlier: 3.687A pdb=" N TRP C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 39 removed outlier: 3.789A pdb=" N ASN C 39 " --> pdb=" O PRO C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 104 removed outlier: 4.132A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS C 96 " --> pdb=" O PRO C 92 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 109 removed outlier: 3.548A pdb=" N ASN C 109 " --> pdb=" O ARG C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.543A pdb=" N VAL C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.583A pdb=" N GLN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.977A pdb=" N VAL C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS C 146 " --> pdb=" O PRO C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 162 removed outlier: 3.845A pdb=" N GLN C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 190 removed outlier: 3.591A pdb=" N LYS C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 24 removed outlier: 4.140A pdb=" N ILE D 6 " --> pdb=" O SER D 2 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR D 7 " --> pdb=" O ALA D 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 23 removed outlier: 4.249A pdb=" N GLU B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 32 removed outlier: 4.279A pdb=" N ARG B 32 " --> pdb=" O ALA B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 32' Processing helix chain 'B' and resid 33 through 56 removed outlier: 3.722A pdb=" N ILE B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 52 " --> pdb=" O CYS B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 102 removed outlier: 4.050A pdb=" N ALA B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ILE B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 99 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.056A pdb=" N MET B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 238 removed outlier: 3.822A pdb=" N LEU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 246 removed outlier: 4.105A pdb=" N TRP B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLY B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 removed outlier: 3.658A pdb=" N ALA B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 270 through 285 removed outlier: 4.014A pdb=" N VAL B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 336 through 344 Processing helix chain 'B' and resid 348 through 355 removed outlier: 4.424A pdb=" N ILE B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 425 removed outlier: 3.846A pdb=" N ASP B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 463 removed outlier: 3.860A pdb=" N ARG B 456 " --> pdb=" O GLY B 452 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 486 removed outlier: 3.853A pdb=" N ALA B 478 " --> pdb=" O ASN B 474 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 479 " --> pdb=" O ARG B 475 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 481 " --> pdb=" O THR B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 504 removed outlier: 3.661A pdb=" N ILE B 503 " --> pdb=" O LYS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 510 removed outlier: 5.137A pdb=" N ALA B 508 " --> pdb=" O GLN B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 527 removed outlier: 4.437A pdb=" N ALA B 525 " --> pdb=" O ASN B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 554 through 557 Processing helix chain 'B' and resid 558 through 566 removed outlier: 4.047A pdb=" N ILE B 564 " --> pdb=" O GLU B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 595 removed outlier: 4.437A pdb=" N ARG B 572 " --> pdb=" O MET B 568 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 575 " --> pdb=" O THR B 571 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 576 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B 581 " --> pdb=" O THR B 577 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B 588 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Proline residue: B 592 - end of helix removed outlier: 3.525A pdb=" N PHE B 595 " --> pdb=" O ILE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 606 removed outlier: 3.526A pdb=" N ASN B 603 " --> pdb=" O PRO B 600 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 630 removed outlier: 4.410A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 638 Processing helix chain 'B' and resid 645 through 656 removed outlier: 3.956A pdb=" N ARG B 651 " --> pdb=" O SER B 647 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP B 655 " --> pdb=" O ARG B 651 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B 656 " --> pdb=" O ARG B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 679 Proline residue: B 665 - end of helix removed outlier: 4.260A pdb=" N LYS B 670 " --> pdb=" O PHE B 666 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 45 removed outlier: 4.049A pdb=" N GLY C 51 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLU C 45 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N VAL C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 131 through 132 Processing sheet with id=AA4, first strand: chain 'B' and resid 131 through 134 removed outlier: 6.718A pdb=" N GLU B 190 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N VAL B 146 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 165 through 166 Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 289 Processing sheet with id=AA7, first strand: chain 'B' and resid 489 through 491 removed outlier: 6.034A pdb=" N THR B 467 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU B 491 " --> pdb=" O THR B 467 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N MET B 469 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B 304 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILE B 470 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU B 306 " --> pdb=" O ILE B 470 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 385 through 386 removed outlier: 4.645A pdb=" N ARG B 394 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL B 434 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU B 435 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1281 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.81 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3056 1.33 - 1.45: 1681 1.45 - 1.57: 6164 1.57 - 1.69: 4 1.69 - 1.81: 110 Bond restraints: 11015 Sorted by residual: bond pdb=" C ASN B 26 " pdb=" N PRO B 27 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.42e+00 bond pdb=" CG LEU A 422 " pdb=" CD2 LEU A 422 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.76e+00 bond pdb=" CB PRO A 425 " pdb=" CG PRO A 425 " ideal model delta sigma weight residual 1.492 1.410 0.082 5.00e-02 4.00e+02 2.68e+00 bond pdb=" CG1 ILE B 267 " pdb=" CD1 ILE B 267 " ideal model delta sigma weight residual 1.513 1.450 0.063 3.90e-02 6.57e+02 2.65e+00 bond pdb=" CB VAL B 231 " pdb=" CG2 VAL B 231 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.45e+00 ... (remaining 11010 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 14331 1.92 - 3.84: 519 3.84 - 5.76: 97 5.76 - 7.68: 36 7.68 - 9.60: 10 Bond angle restraints: 14993 Sorted by residual: angle pdb=" N ILE A 398 " pdb=" CA ILE A 398 " pdb=" C ILE A 398 " ideal model delta sigma weight residual 113.71 105.24 8.47 9.50e-01 1.11e+00 7.94e+01 angle pdb=" N ILE D 24 " pdb=" CA ILE D 24 " pdb=" C ILE D 24 " ideal model delta sigma weight residual 112.29 107.96 4.33 9.40e-01 1.13e+00 2.12e+01 angle pdb=" C PRO B 11 " pdb=" N THR B 12 " pdb=" CA THR B 12 " ideal model delta sigma weight residual 121.54 130.31 -8.77 1.91e+00 2.74e-01 2.11e+01 angle pdb=" C PHE A 260 " pdb=" CA PHE A 260 " pdb=" CB PHE A 260 " ideal model delta sigma weight residual 111.22 106.62 4.60 1.23e+00 6.61e-01 1.40e+01 angle pdb=" C ASN B 316 " pdb=" N ARG B 317 " pdb=" CA ARG B 317 " ideal model delta sigma weight residual 122.07 127.36 -5.29 1.43e+00 4.89e-01 1.37e+01 ... (remaining 14988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.27: 6240 15.27 - 30.54: 245 30.54 - 45.81: 55 45.81 - 61.09: 6 61.09 - 76.36: 8 Dihedral angle restraints: 6554 sinusoidal: 2446 harmonic: 4108 Sorted by residual: dihedral pdb=" CA VAL B 449 " pdb=" C VAL B 449 " pdb=" N LYS B 450 " pdb=" CA LYS B 450 " ideal model delta harmonic sigma weight residual -180.00 -151.47 -28.53 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ASP B 447 " pdb=" C ASP B 447 " pdb=" N ILE B 448 " pdb=" CA ILE B 448 " ideal model delta harmonic sigma weight residual -180.00 -151.72 -28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA PHE B 412 " pdb=" C PHE B 412 " pdb=" N PRO B 413 " pdb=" CA PRO B 413 " ideal model delta harmonic sigma weight residual 180.00 151.99 28.01 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 6551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1659 0.092 - 0.183: 144 0.183 - 0.275: 5 0.275 - 0.367: 0 0.367 - 0.458: 1 Chirality restraints: 1809 Sorted by residual: chirality pdb=" CB ILE A 368 " pdb=" CA ILE A 368 " pdb=" CG1 ILE A 368 " pdb=" CG2 ILE A 368 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CG LEU A 133 " pdb=" CB LEU A 133 " pdb=" CD1 LEU A 133 " pdb=" CD2 LEU A 133 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1806 not shown) Planarity restraints: 1902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 447 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO A 448 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 448 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 448 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 215 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO B 216 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 216 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 216 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 523 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO B 524 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 524 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 524 " 0.032 5.00e-02 4.00e+02 ... (remaining 1899 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 3219 2.81 - 3.39: 11737 3.39 - 3.97: 20410 3.97 - 4.56: 28723 4.56 - 5.14: 41943 Nonbonded interactions: 106032 Sorted by model distance: nonbonded pdb=" OG SER B 175 " pdb=" O GLY B 538 " model vdw 2.227 3.040 nonbonded pdb=" O VAL A 107 " pdb=" OG1 THR A 111 " model vdw 2.241 3.040 nonbonded pdb=" O LEU A 541 " pdb=" OH TYR B 587 " model vdw 2.264 3.040 nonbonded pdb=" OG SER B 192 " pdb=" OE1 GLN B 540 " model vdw 2.278 3.040 nonbonded pdb=" OG SER A 343 " pdb=" O ASN A 466 " model vdw 2.298 3.040 ... (remaining 106027 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.120 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 11015 Z= 0.279 Angle : 0.926 9.600 14993 Z= 0.488 Chirality : 0.054 0.458 1809 Planarity : 0.007 0.069 1902 Dihedral : 9.853 76.358 3914 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.18 % Allowed : 3.08 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.34 (0.16), residues: 1439 helix: -4.02 (0.10), residues: 737 sheet: -2.86 (0.50), residues: 70 loop : -2.85 (0.21), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 172 TYR 0.026 0.003 TYR B 587 PHE 0.035 0.003 PHE A 109 TRP 0.035 0.003 TRP A 364 HIS 0.011 0.002 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00668 (11015) covalent geometry : angle 0.92645 (14993) hydrogen bonds : bond 0.29313 ( 444) hydrogen bonds : angle 10.56964 ( 1281) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 253 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 TYR cc_start: 0.8982 (p90) cc_final: 0.8660 (p90) REVERT: A 458 TYR cc_start: 0.9066 (t80) cc_final: 0.8571 (t80) REVERT: C 5 ARG cc_start: 0.7959 (mtt180) cc_final: 0.7475 (ttt180) REVERT: C 119 GLU cc_start: 0.9232 (mp0) cc_final: 0.8991 (mp0) REVERT: C 130 ASN cc_start: 0.8995 (t0) cc_final: 0.8780 (t0) REVERT: C 189 ASP cc_start: 0.8356 (t0) cc_final: 0.7980 (t70) REVERT: B 131 ILE cc_start: 0.8489 (mm) cc_final: 0.8206 (pt) REVERT: B 317 ARG cc_start: 0.8401 (ptt180) cc_final: 0.8144 (ttt180) REVERT: B 359 ARG cc_start: 0.7265 (ttm-80) cc_final: 0.6961 (ptt-90) REVERT: B 448 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8123 (mm) REVERT: B 530 ASP cc_start: 0.7942 (m-30) cc_final: 0.7677 (m-30) REVERT: B 535 MET cc_start: 0.8789 (mmp) cc_final: 0.8249 (mmt) REVERT: B 619 SER cc_start: 0.8949 (m) cc_final: 0.8584 (t) REVERT: B 649 MET cc_start: 0.8375 (ttt) cc_final: 0.8030 (ttt) REVERT: B 669 ILE cc_start: 0.8974 (mm) cc_final: 0.8691 (mm) outliers start: 2 outliers final: 0 residues processed: 255 average time/residue: 0.1124 time to fit residues: 40.2264 Evaluate side-chains 129 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 448 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.0010 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 85 HIS ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN B 30 GLN B 211 GLN B 404 HIS ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 GLN B 554 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.096399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.069675 restraints weight = 28298.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.071564 restraints weight = 12664.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.072639 restraints weight = 7471.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.073376 restraints weight = 5449.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.073804 restraints weight = 4515.930| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11015 Z= 0.138 Angle : 0.651 9.033 14993 Z= 0.333 Chirality : 0.042 0.162 1809 Planarity : 0.005 0.047 1902 Dihedral : 5.796 32.789 1529 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.20 % Allowed : 9.95 % Favored : 87.85 % 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 aren not related in a simple way. whole: -3.70 (0.19), residues: 1439 helix: -2.32 (0.15), residues: 782 sheet: -2.33 (0.54), residues: 74 loop : -2.48 (0.23), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 425 TYR 0.019 0.001 TYR A 381 PHE 0.023 0.002 PHE C 11 TRP 0.028 0.001 TRP A 167 HIS 0.004 0.001 HIS B 563 Details of bonding type rmsd covalent geometry : bond 0.00312 (11015) covalent geometry : angle 0.65105 (14993) hydrogen bonds : bond 0.04554 ( 444) hydrogen bonds : angle 5.98225 ( 1281) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.9088 (mtmt) cc_final: 0.8876 (mtmm) REVERT: A 118 TYR cc_start: 0.8841 (p90) cc_final: 0.8577 (p90) REVERT: A 357 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9426 (tm) REVERT: C 50 ARG cc_start: 0.8174 (mmt180) cc_final: 0.7712 (mmt180) REVERT: C 129 ASP cc_start: 0.8184 (t0) cc_final: 0.7975 (t0) REVERT: C 130 ASN cc_start: 0.8664 (t0) cc_final: 0.8448 (t0) REVERT: C 190 GLU cc_start: 0.6548 (mm-30) cc_final: 0.6058 (mm-30) REVERT: B 58 MET cc_start: 0.6453 (ptp) cc_final: 0.6159 (ptp) REVERT: B 187 LEU cc_start: 0.8726 (mt) cc_final: 0.8059 (tp) REVERT: B 317 ARG cc_start: 0.8369 (ptt180) cc_final: 0.8159 (ttt180) REVERT: B 359 ARG cc_start: 0.7350 (ttm-80) cc_final: 0.6927 (ptt180) REVERT: B 448 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8097 (mm) REVERT: B 535 MET cc_start: 0.9029 (mmp) cc_final: 0.8524 (mmt) REVERT: B 619 SER cc_start: 0.9060 (m) cc_final: 0.8759 (t) REVERT: B 669 ILE cc_start: 0.9274 (mm) cc_final: 0.8550 (mm) outliers start: 25 outliers final: 8 residues processed: 186 average time/residue: 0.1061 time to fit residues: 27.9748 Evaluate side-chains 135 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 632 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 126 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 104 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.093595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.066415 restraints weight = 28660.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.068257 restraints weight = 13009.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.069401 restraints weight = 7754.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.069969 restraints weight = 5666.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.070350 restraints weight = 4782.177| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11015 Z= 0.202 Angle : 0.659 10.441 14993 Z= 0.329 Chirality : 0.043 0.144 1809 Planarity : 0.004 0.040 1902 Dihedral : 5.385 33.811 1529 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.99 % Allowed : 11.09 % Favored : 85.92 % 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 aren not related in a simple way. whole: -2.75 (0.21), residues: 1439 helix: -1.45 (0.18), residues: 788 sheet: -2.03 (0.60), residues: 62 loop : -2.19 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 167 TYR 0.017 0.002 TYR A 381 PHE 0.017 0.002 PHE C 11 TRP 0.029 0.001 TRP A 167 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00468 (11015) covalent geometry : angle 0.65934 (14993) hydrogen bonds : bond 0.03986 ( 444) hydrogen bonds : angle 5.40497 ( 1281) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 TYR cc_start: 0.8912 (p90) cc_final: 0.8649 (p90) REVERT: A 347 VAL cc_start: 0.8805 (t) cc_final: 0.8252 (m) REVERT: C 130 ASN cc_start: 0.8857 (t0) cc_final: 0.8443 (t0) REVERT: C 146 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8715 (ptmt) REVERT: C 189 ASP cc_start: 0.7723 (t0) cc_final: 0.7456 (t0) REVERT: B 58 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.6487 (ptp) REVERT: B 187 LEU cc_start: 0.8881 (mt) cc_final: 0.8228 (tp) REVERT: B 317 ARG cc_start: 0.8451 (ptt180) cc_final: 0.8139 (ttt180) REVERT: B 359 ARG cc_start: 0.7518 (ttm-80) cc_final: 0.6969 (ptt180) REVERT: B 448 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8135 (mm) REVERT: B 535 MET cc_start: 0.8983 (mmp) cc_final: 0.8600 (mmt) REVERT: B 619 SER cc_start: 0.9070 (m) cc_final: 0.8800 (t) outliers start: 34 outliers final: 13 residues processed: 163 average time/residue: 0.1003 time to fit residues: 23.7565 Evaluate side-chains 143 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 632 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 95 optimal weight: 0.0670 chunk 62 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.095350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.068505 restraints weight = 28481.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.070437 restraints weight = 12719.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.071547 restraints weight = 7448.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.072230 restraints weight = 5412.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.072666 restraints weight = 4515.716| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11015 Z= 0.123 Angle : 0.601 10.085 14993 Z= 0.293 Chirality : 0.041 0.146 1809 Planarity : 0.004 0.035 1902 Dihedral : 5.065 34.055 1529 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.82 % Allowed : 11.62 % Favored : 85.56 % 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 aren not related in a simple way. whole: -2.26 (0.22), residues: 1439 helix: -0.94 (0.19), residues: 786 sheet: -2.15 (0.52), residues: 79 loop : -2.08 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 181 TYR 0.017 0.001 TYR A 381 PHE 0.029 0.001 PHE C 11 TRP 0.021 0.001 TRP A 167 HIS 0.004 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00291 (11015) covalent geometry : angle 0.60054 (14993) hydrogen bonds : bond 0.03403 ( 444) hydrogen bonds : angle 4.99292 ( 1281) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 TYR cc_start: 0.8792 (p90) cc_final: 0.8583 (p90) REVERT: A 282 MET cc_start: 0.9174 (ppp) cc_final: 0.8825 (ppp) REVERT: A 302 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8435 (mm-30) REVERT: A 347 VAL cc_start: 0.8695 (t) cc_final: 0.8097 (m) REVERT: C 189 ASP cc_start: 0.7777 (t0) cc_final: 0.7546 (t0) REVERT: B 58 MET cc_start: 0.6709 (OUTLIER) cc_final: 0.6479 (ptp) REVERT: B 187 LEU cc_start: 0.8768 (mt) cc_final: 0.8123 (tp) REVERT: B 359 ARG cc_start: 0.7500 (ttm-80) cc_final: 0.6928 (ptt180) REVERT: B 448 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8126 (mm) REVERT: B 515 MET cc_start: 0.8443 (tpp) cc_final: 0.8113 (tpp) REVERT: B 535 MET cc_start: 0.8975 (mmp) cc_final: 0.8689 (mmt) REVERT: B 624 ASN cc_start: 0.8832 (OUTLIER) cc_final: 0.8629 (t0) REVERT: B 669 ILE cc_start: 0.9205 (mm) cc_final: 0.8764 (mm) outliers start: 32 outliers final: 12 residues processed: 170 average time/residue: 0.1057 time to fit residues: 25.8244 Evaluate side-chains 143 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 624 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 32 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 133 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 85 optimal weight: 30.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.092685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.065596 restraints weight = 28592.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.067490 restraints weight = 12478.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.068545 restraints weight = 7248.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.069250 restraints weight = 5281.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.069675 restraints weight = 4360.114| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11015 Z= 0.152 Angle : 0.605 9.719 14993 Z= 0.297 Chirality : 0.042 0.162 1809 Planarity : 0.004 0.035 1902 Dihedral : 4.920 33.972 1529 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.29 % Allowed : 12.68 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.22), residues: 1439 helix: -0.66 (0.19), residues: 782 sheet: -2.07 (0.52), residues: 81 loop : -1.94 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 425 TYR 0.016 0.002 TYR A 381 PHE 0.027 0.001 PHE C 11 TRP 0.021 0.001 TRP A 167 HIS 0.002 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00357 (11015) covalent geometry : angle 0.60480 (14993) hydrogen bonds : bond 0.03393 ( 444) hydrogen bonds : angle 4.86217 ( 1281) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 TYR cc_start: 0.8876 (p90) cc_final: 0.8663 (p90) REVERT: A 302 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8623 (mm-30) REVERT: A 347 VAL cc_start: 0.8915 (t) cc_final: 0.8566 (p) REVERT: C 130 ASN cc_start: 0.8835 (t0) cc_final: 0.8553 (t0) REVERT: C 189 ASP cc_start: 0.7840 (t0) cc_final: 0.7611 (t0) REVERT: B 58 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6644 (ptp) REVERT: B 187 LEU cc_start: 0.8891 (mt) cc_final: 0.8357 (tp) REVERT: B 279 MET cc_start: 0.8677 (mmt) cc_final: 0.8354 (mmm) REVERT: B 359 ARG cc_start: 0.7477 (ttm-80) cc_final: 0.6887 (ptt180) REVERT: B 448 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.7981 (mm) REVERT: B 469 MET cc_start: 0.8644 (tmm) cc_final: 0.8213 (tmm) REVERT: B 515 MET cc_start: 0.8561 (tpp) cc_final: 0.8177 (tpp) REVERT: B 535 MET cc_start: 0.8988 (mmp) cc_final: 0.8702 (mmt) REVERT: B 619 SER cc_start: 0.9175 (m) cc_final: 0.8868 (t) REVERT: B 624 ASN cc_start: 0.8905 (OUTLIER) cc_final: 0.8646 (t0) outliers start: 26 outliers final: 13 residues processed: 156 average time/residue: 0.0949 time to fit residues: 22.0575 Evaluate side-chains 142 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 624 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 16 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 40 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN B 80 ASN B 404 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.093944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.067014 restraints weight = 28508.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.068925 restraints weight = 12368.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.070173 restraints weight = 7201.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.070789 restraints weight = 5076.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.071166 restraints weight = 4223.263| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11015 Z= 0.116 Angle : 0.584 11.347 14993 Z= 0.286 Chirality : 0.040 0.144 1809 Planarity : 0.003 0.034 1902 Dihedral : 4.785 33.654 1529 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.55 % Allowed : 12.59 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.22), residues: 1439 helix: -0.46 (0.19), residues: 795 sheet: -1.98 (0.53), residues: 80 loop : -1.96 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 425 TYR 0.017 0.001 TYR A 201 PHE 0.027 0.001 PHE C 11 TRP 0.023 0.001 TRP A 167 HIS 0.004 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00274 (11015) covalent geometry : angle 0.58406 (14993) hydrogen bonds : bond 0.03156 ( 444) hydrogen bonds : angle 4.66587 ( 1281) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 TYR cc_start: 0.8798 (m-10) cc_final: 0.8286 (m-10) REVERT: A 148 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.8874 (tp) REVERT: A 302 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8534 (mm-30) REVERT: A 347 VAL cc_start: 0.8870 (t) cc_final: 0.8510 (p) REVERT: C 130 ASN cc_start: 0.8840 (t0) cc_final: 0.8516 (t0) REVERT: C 189 ASP cc_start: 0.7815 (t0) cc_final: 0.7592 (t0) REVERT: B 58 MET cc_start: 0.6774 (OUTLIER) cc_final: 0.6455 (ptp) REVERT: B 187 LEU cc_start: 0.8890 (mt) cc_final: 0.8365 (tp) REVERT: B 359 ARG cc_start: 0.7498 (ttm-80) cc_final: 0.6853 (ptt180) REVERT: B 448 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8014 (mm) REVERT: B 469 MET cc_start: 0.8639 (tmm) cc_final: 0.8179 (tmm) REVERT: B 515 MET cc_start: 0.8479 (tpp) cc_final: 0.8275 (tpp) REVERT: B 535 MET cc_start: 0.8943 (mmp) cc_final: 0.8688 (mmt) REVERT: B 619 SER cc_start: 0.9120 (m) cc_final: 0.8889 (t) REVERT: B 624 ASN cc_start: 0.8876 (OUTLIER) cc_final: 0.8607 (t0) outliers start: 29 outliers final: 11 residues processed: 170 average time/residue: 0.0956 time to fit residues: 24.3879 Evaluate side-chains 147 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 624 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 6.9990 chunk 87 optimal weight: 30.0000 chunk 71 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.094570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.067263 restraints weight = 28656.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.069267 restraints weight = 12535.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.070373 restraints weight = 7269.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.071183 restraints weight = 5267.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.071384 restraints weight = 4284.879| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11015 Z= 0.118 Angle : 0.600 10.746 14993 Z= 0.290 Chirality : 0.041 0.139 1809 Planarity : 0.003 0.032 1902 Dihedral : 4.703 32.870 1529 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.73 % Allowed : 13.29 % Favored : 83.98 % 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 aren not related in a simple way. whole: -1.49 (0.22), residues: 1439 helix: -0.23 (0.19), residues: 788 sheet: -1.89 (0.54), residues: 81 loop : -1.85 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 425 TYR 0.016 0.002 TYR A 381 PHE 0.027 0.001 PHE C 11 TRP 0.023 0.001 TRP A 167 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00280 (11015) covalent geometry : angle 0.59979 (14993) hydrogen bonds : bond 0.03103 ( 444) hydrogen bonds : angle 4.59029 ( 1281) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 TYR cc_start: 0.8770 (m-10) cc_final: 0.8253 (m-10) REVERT: A 148 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.8890 (tp) REVERT: A 347 VAL cc_start: 0.8949 (t) cc_final: 0.8618 (p) REVERT: C 130 ASN cc_start: 0.8785 (t0) cc_final: 0.8403 (t0) REVERT: C 189 ASP cc_start: 0.7787 (t0) cc_final: 0.7549 (t0) REVERT: B 58 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.6343 (ptp) REVERT: B 359 ARG cc_start: 0.7461 (ttm-80) cc_final: 0.6877 (ptt-90) REVERT: B 448 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7921 (mm) REVERT: B 515 MET cc_start: 0.8553 (tpp) cc_final: 0.8202 (tpp) REVERT: B 535 MET cc_start: 0.8923 (mmp) cc_final: 0.8654 (mmt) REVERT: B 619 SER cc_start: 0.9117 (m) cc_final: 0.8813 (t) REVERT: B 624 ASN cc_start: 0.8881 (OUTLIER) cc_final: 0.8650 (t0) outliers start: 31 outliers final: 15 residues processed: 170 average time/residue: 0.0964 time to fit residues: 24.4343 Evaluate side-chains 153 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 624 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 44 optimal weight: 0.0370 chunk 68 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.095008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.067933 restraints weight = 28560.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.069935 restraints weight = 12466.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.071045 restraints weight = 7197.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.071828 restraints weight = 5201.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.072023 restraints weight = 4255.369| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11015 Z= 0.114 Angle : 0.599 10.456 14993 Z= 0.291 Chirality : 0.041 0.140 1809 Planarity : 0.003 0.034 1902 Dihedral : 4.647 32.004 1529 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.29 % Allowed : 14.52 % Favored : 83.19 % 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 aren not related in a simple way. whole: -1.34 (0.22), residues: 1439 helix: -0.09 (0.19), residues: 786 sheet: -1.88 (0.53), residues: 83 loop : -1.78 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 278 TYR 0.016 0.002 TYR A 381 PHE 0.016 0.001 PHE A 527 TRP 0.033 0.001 TRP A 167 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00269 (11015) covalent geometry : angle 0.59946 (14993) hydrogen bonds : bond 0.03023 ( 444) hydrogen bonds : angle 4.54332 ( 1281) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 TYR cc_start: 0.8758 (m-10) cc_final: 0.8263 (m-10) REVERT: A 148 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.8899 (tp) REVERT: A 227 MET cc_start: 0.8360 (mmm) cc_final: 0.7505 (mpp) REVERT: A 347 VAL cc_start: 0.8932 (t) cc_final: 0.8618 (p) REVERT: C 130 ASN cc_start: 0.8738 (t0) cc_final: 0.8340 (t0) REVERT: C 189 ASP cc_start: 0.7701 (t0) cc_final: 0.7466 (t0) REVERT: B 58 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6489 (ptt) REVERT: B 359 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.6877 (ptt-90) REVERT: B 448 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7654 (mm) REVERT: B 515 MET cc_start: 0.8401 (tpp) cc_final: 0.8135 (tpp) REVERT: B 535 MET cc_start: 0.8883 (mmp) cc_final: 0.8624 (mmt) REVERT: B 619 SER cc_start: 0.9027 (m) cc_final: 0.8781 (t) REVERT: B 624 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8662 (t0) outliers start: 26 outliers final: 16 residues processed: 157 average time/residue: 0.0945 time to fit residues: 22.2776 Evaluate side-chains 151 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 624 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 9 optimal weight: 0.0070 chunk 76 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 121 optimal weight: 9.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.095288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.068757 restraints weight = 28516.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.070737 restraints weight = 12268.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.071842 restraints weight = 6989.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.072600 restraints weight = 5031.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.072946 restraints weight = 4130.356| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11015 Z= 0.113 Angle : 0.609 9.784 14993 Z= 0.294 Chirality : 0.041 0.136 1809 Planarity : 0.003 0.032 1902 Dihedral : 4.547 30.910 1529 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.02 % Allowed : 14.79 % Favored : 83.19 % 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 aren not related in a simple way. whole: -1.16 (0.22), residues: 1439 helix: 0.06 (0.19), residues: 787 sheet: -1.81 (0.52), residues: 83 loop : -1.71 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 143 TYR 0.016 0.002 TYR A 381 PHE 0.014 0.001 PHE A 527 TRP 0.033 0.001 TRP A 167 HIS 0.001 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00269 (11015) covalent geometry : angle 0.60912 (14993) hydrogen bonds : bond 0.02983 ( 444) hydrogen bonds : angle 4.46651 ( 1281) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 TYR cc_start: 0.8761 (m-10) cc_final: 0.8241 (m-10) REVERT: A 148 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.8893 (tp) REVERT: A 227 MET cc_start: 0.8288 (mmm) cc_final: 0.7450 (mpp) REVERT: A 282 MET cc_start: 0.8976 (tmm) cc_final: 0.8732 (tmm) REVERT: A 347 VAL cc_start: 0.8932 (t) cc_final: 0.8618 (p) REVERT: C 119 GLU cc_start: 0.8633 (mp0) cc_final: 0.8345 (mt-10) REVERT: C 130 ASN cc_start: 0.8704 (t0) cc_final: 0.8235 (t0) REVERT: C 189 ASP cc_start: 0.7615 (t0) cc_final: 0.7390 (t0) REVERT: B 58 MET cc_start: 0.6741 (ptp) cc_final: 0.6537 (ptp) REVERT: B 359 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.6860 (ptt180) REVERT: B 448 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7674 (mm) REVERT: B 515 MET cc_start: 0.8348 (tpp) cc_final: 0.8077 (tpp) REVERT: B 535 MET cc_start: 0.8844 (mmp) cc_final: 0.8584 (mmt) REVERT: B 619 SER cc_start: 0.9006 (m) cc_final: 0.8761 (t) REVERT: B 649 MET cc_start: 0.9044 (tmm) cc_final: 0.7394 (tmm) outliers start: 23 outliers final: 16 residues processed: 154 average time/residue: 0.0967 time to fit residues: 22.0933 Evaluate side-chains 146 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 449 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 88 optimal weight: 0.2980 chunk 56 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 65 optimal weight: 0.0020 chunk 27 optimal weight: 0.0770 chunk 55 optimal weight: 0.0070 chunk 30 optimal weight: 0.0000 overall best weight: 0.0768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN A 465 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.097731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.071217 restraints weight = 28500.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.073266 restraints weight = 12301.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.074535 restraints weight = 7054.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.075097 restraints weight = 4989.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.075532 restraints weight = 4178.747| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11015 Z= 0.105 Angle : 0.627 13.801 14993 Z= 0.296 Chirality : 0.040 0.136 1809 Planarity : 0.003 0.032 1902 Dihedral : 4.472 29.445 1529 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.41 % Allowed : 15.32 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.22), residues: 1439 helix: 0.21 (0.19), residues: 789 sheet: -2.05 (0.48), residues: 95 loop : -1.69 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 143 TYR 0.020 0.002 TYR B 657 PHE 0.018 0.001 PHE B 322 TRP 0.032 0.001 TRP A 167 HIS 0.001 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00236 (11015) covalent geometry : angle 0.62702 (14993) hydrogen bonds : bond 0.02873 ( 444) hydrogen bonds : angle 4.35431 ( 1281) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 TYR cc_start: 0.8625 (m-10) cc_final: 0.8254 (m-80) REVERT: A 148 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.8854 (tp) REVERT: A 347 VAL cc_start: 0.8821 (t) cc_final: 0.8497 (p) REVERT: A 536 LEU cc_start: 0.8679 (tt) cc_final: 0.8135 (mp) REVERT: C 119 GLU cc_start: 0.8564 (mp0) cc_final: 0.8284 (mt-10) REVERT: C 130 ASN cc_start: 0.8645 (t0) cc_final: 0.8139 (t0) REVERT: B 58 MET cc_start: 0.6888 (ptp) cc_final: 0.6638 (ptp) REVERT: B 187 LEU cc_start: 0.8876 (mt) cc_final: 0.8342 (tp) REVERT: B 279 MET cc_start: 0.8565 (mmt) cc_final: 0.8220 (mmm) REVERT: B 359 ARG cc_start: 0.7456 (ttm-80) cc_final: 0.6840 (ptt180) REVERT: B 448 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7826 (mm) REVERT: B 515 MET cc_start: 0.8279 (tpp) cc_final: 0.8032 (tpp) REVERT: B 535 MET cc_start: 0.8802 (mmp) cc_final: 0.8464 (mmt) REVERT: B 619 SER cc_start: 0.8942 (m) cc_final: 0.8730 (t) REVERT: B 649 MET cc_start: 0.9043 (tmm) cc_final: 0.7433 (tmm) outliers start: 16 outliers final: 10 residues processed: 167 average time/residue: 0.0985 time to fit residues: 24.3274 Evaluate side-chains 154 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain B residue 448 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 101 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 119 optimal weight: 0.0270 chunk 48 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 26 optimal weight: 0.0070 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN A 513 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.095555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.069339 restraints weight = 28881.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.071251 restraints weight = 12798.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.072463 restraints weight = 7476.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.073090 restraints weight = 5325.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.073347 restraints weight = 4417.511| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11015 Z= 0.107 Angle : 0.621 12.837 14993 Z= 0.298 Chirality : 0.041 0.183 1809 Planarity : 0.004 0.035 1902 Dihedral : 4.392 28.201 1529 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.14 % Allowed : 16.20 % Favored : 82.66 % 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 aren not related in a simple way. whole: -0.88 (0.22), residues: 1439 helix: 0.41 (0.19), residues: 776 sheet: -1.93 (0.48), residues: 95 loop : -1.70 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 425 TYR 0.020 0.002 TYR C 170 PHE 0.025 0.001 PHE B 322 TRP 0.041 0.001 TRP A 167 HIS 0.001 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00253 (11015) covalent geometry : angle 0.62104 (14993) hydrogen bonds : bond 0.02876 ( 444) hydrogen bonds : angle 4.32481 ( 1281) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1976.70 seconds wall clock time: 34 minutes 52.83 seconds (2092.83 seconds total)