Starting phenix.real_space_refine on Wed Mar 4 06:48:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6owt_20217/03_2026/6owt_20217.cif Found real_map, /net/cci-nas-00/data/ceres_data/6owt_20217/03_2026/6owt_20217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6owt_20217/03_2026/6owt_20217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6owt_20217/03_2026/6owt_20217.map" model { file = "/net/cci-nas-00/data/ceres_data/6owt_20217/03_2026/6owt_20217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6owt_20217/03_2026/6owt_20217.cif" } resolution = 3.8 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= 0.003 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 32 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 7498 2.51 5 N 1975 2.21 5 O 2130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11649 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4255 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 22, 'TRANS': 567} Unresolved non-hydrogen bonds: 418 Unresolved non-hydrogen angles: 512 Unresolved non-hydrogen dihedrals: 344 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ARG:plan': 12, 'ASN:plan1': 8, 'GLU:plan': 13, 'PHE:plan': 4, 'ASP:plan': 11, 'TYR:plan': 2, 'HIS:plan': 3, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 234 Chain: "B" Number of atoms: 4242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4242 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 26, 'TRANS': 551} Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 421 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASN:plan1': 11, 'GLU:plan': 16, 'ASP:plan': 17, 'ARG:plan': 5, 'TYR:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 202 Chain: "M" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 932 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 121} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 5, 'ARG:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "T" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 74 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1047 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "S" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1099 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 139} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'GLU:plan': 4, 'ARG:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 60 Time building chain proxies: 2.88, per 1000 atoms: 0.25 Number of scatterers: 11649 At special positions: 0 Unit cell: (98.814, 105.708, 127.539, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 2130 8.00 N 1975 7.00 C 7498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS N 193 " - pdb=" SG CYS S 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 639.3 milliseconds 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3048 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 4 sheets defined 68.1% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 51 through 68 Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 82 through 85 removed outlier: 3.677A pdb=" N SER A 85 " --> pdb=" O LEU A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 106 through 122 Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 149 through 156 removed outlier: 3.748A pdb=" N LYS A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 179 removed outlier: 3.814A pdb=" N LYS A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.764A pdb=" N THR A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 222 through 238 removed outlier: 3.749A pdb=" N VAL A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER A 227 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.622A pdb=" N CYS A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 293 Processing helix chain 'A' and resid 299 through 321 removed outlier: 4.264A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 removed outlier: 3.556A pdb=" N ARG A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 352 removed outlier: 4.311A pdb=" N LEU A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.533A pdb=" N SER A 358 " --> pdb=" O CYS A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 382 through 397 Processing helix chain 'A' and resid 401 through 414 Processing helix chain 'A' and resid 420 through 435 removed outlier: 3.840A pdb=" N ILE A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 452 removed outlier: 4.115A pdb=" N TYR A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 removed outlier: 4.104A pdb=" N TRP A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 509 through 512 removed outlier: 3.593A pdb=" N ALA A 512 " --> pdb=" O ASN A 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 512' Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 518 through 531 removed outlier: 3.913A pdb=" N LEU A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS A 531 " --> pdb=" O HIS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.585A pdb=" N LEU A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 565 removed outlier: 3.684A pdb=" N ILE A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 573 through 587 Processing helix chain 'A' and resid 591 through 599 Processing helix chain 'A' and resid 610 through 620 Processing helix chain 'B' and resid 17 through 24 removed outlier: 3.705A pdb=" N GLU B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 44 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 55 Processing helix chain 'B' and resid 62 through 76 Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 87 through 93 Processing helix chain 'B' and resid 99 through 111 Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 122 through 128 Processing helix chain 'B' and resid 134 through 149 removed outlier: 3.671A pdb=" N ARG B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 170 removed outlier: 3.961A pdb=" N ALA B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 188 Processing helix chain 'B' and resid 199 through 213 removed outlier: 4.927A pdb=" N ASN B 205 " --> pdb=" O PRO B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 228 removed outlier: 4.221A pdb=" N PHE B 221 " --> pdb=" O TRP B 217 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 245 Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 274 through 291 removed outlier: 3.572A pdb=" N ASN B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Proline residue: B 286 - end of helix Processing helix chain 'B' and resid 295 through 313 removed outlier: 3.746A pdb=" N LEU B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.872A pdb=" N PHE B 325 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.654A pdb=" N LEU B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 361 removed outlier: 3.793A pdb=" N ALA B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU B 357 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 366 through 384 removed outlier: 4.104A pdb=" N GLY B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.830A pdb=" N GLN B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 413 " --> pdb=" O GLU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 436 removed outlier: 4.228A pdb=" N GLU B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 436 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 454 Processing helix chain 'B' and resid 461 through 472 removed outlier: 4.121A pdb=" N LEU B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 490 through 495 Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 504 through 512 removed outlier: 3.686A pdb=" N GLN B 512 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 531 removed outlier: 3.745A pdb=" N SER B 531 " --> pdb=" O TRP B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 Processing helix chain 'B' and resid 556 through 566 removed outlier: 4.082A pdb=" N CYS B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS B 566 " --> pdb=" O GLU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 575 removed outlier: 4.079A pdb=" N VAL B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 581 removed outlier: 4.008A pdb=" N PHE B 581 " --> pdb=" O PRO B 578 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 36 removed outlier: 3.980A pdb=" N PHE M 32 " --> pdb=" O ALA M 28 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG M 33 " --> pdb=" O VAL M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 removed outlier: 3.945A pdb=" N VAL M 78 " --> pdb=" O ASN M 74 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE M 79 " --> pdb=" O ALA M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 104 through 116 removed outlier: 3.577A pdb=" N TYR M 109 " --> pdb=" O PHE M 105 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU M 114 " --> pdb=" O GLU M 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU M 116 " --> pdb=" O LEU M 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 22 Processing helix chain 'N' and resid 112 through 127 Processing helix chain 'N' and resid 135 through 150 Processing helix chain 'N' and resid 217 through 221 removed outlier: 3.589A pdb=" N TYR N 221 " --> pdb=" O LYS N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 224 through 229 removed outlier: 3.583A pdb=" N TYR N 229 " --> pdb=" O ALA N 225 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 40 removed outlier: 3.598A pdb=" N ILE S 32 " --> pdb=" O LYS S 28 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU S 33 " --> pdb=" O GLN S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 95 removed outlier: 4.084A pdb=" N PHE S 95 " --> pdb=" O LEU S 91 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 106 Processing helix chain 'S' and resid 106 through 117 removed outlier: 3.534A pdb=" N THR S 112 " --> pdb=" O TYR S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 138 Processing sheet with id=AA1, first strand: chain 'B' and resid 8 through 9 removed outlier: 6.423A pdb=" N THR B 8 " --> pdb=" O ASN N 181 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL N 178 " --> pdb=" O ALA N 212 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA N 212 " --> pdb=" O VAL N 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 14 through 16 removed outlier: 6.801A pdb=" N ILE M 7 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.525A pdb=" N ILE S 7 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA S 17 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE S 5 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TRP S 19 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ARG S 3 " --> pdb=" O TRP S 19 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE S 4 " --> pdb=" O CYS S 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 118 through 119 677 hydrogen bonds defined for protein. 2001 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: 1.96 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3820 1.34 - 1.46: 2333 1.46 - 1.58: 5653 1.58 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 11872 Sorted by residual: bond pdb=" C THR B 245 " pdb=" N PRO B 246 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.92e+00 bond pdb=" C PRO B 286 " pdb=" N PRO B 287 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.20e-02 6.94e+03 2.11e+00 bond pdb=" C GLU B 124 " pdb=" N PRO B 125 " ideal model delta sigma weight residual 1.336 1.352 -0.016 1.25e-02 6.40e+03 1.71e+00 bond pdb=" CA THR B 245 " pdb=" C THR B 245 " ideal model delta sigma weight residual 1.522 1.538 -0.016 1.26e-02 6.30e+03 1.70e+00 bond pdb=" C ILE A 151 " pdb=" N PRO A 152 " ideal model delta sigma weight residual 1.336 1.352 -0.016 1.23e-02 6.61e+03 1.69e+00 ... (remaining 11867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 16042 2.29 - 4.58: 167 4.58 - 6.87: 12 6.87 - 9.16: 6 9.16 - 11.45: 1 Bond angle restraints: 16228 Sorted by residual: angle pdb=" C ARG M 60 " pdb=" N SER M 61 " pdb=" CA SER M 61 " ideal model delta sigma weight residual 121.54 128.54 -7.00 1.91e+00 2.74e-01 1.34e+01 angle pdb=" N ASN B 200 " pdb=" CA ASN B 200 " pdb=" C ASN B 200 " ideal model delta sigma weight residual 109.81 117.66 -7.85 2.21e+00 2.05e-01 1.26e+01 angle pdb=" CA PRO B 286 " pdb=" C PRO B 286 " pdb=" N PRO B 287 " ideal model delta sigma weight residual 117.93 121.99 -4.06 1.20e+00 6.94e-01 1.15e+01 angle pdb=" CA LEU B 482 " pdb=" CB LEU B 482 " pdb=" CG LEU B 482 " ideal model delta sigma weight residual 116.30 127.75 -11.45 3.50e+00 8.16e-02 1.07e+01 angle pdb=" CA ALA B 285 " pdb=" C ALA B 285 " pdb=" N PRO B 286 " ideal model delta sigma weight residual 118.44 123.05 -4.61 1.59e+00 3.96e-01 8.39e+00 ... (remaining 16223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 6658 17.86 - 35.71: 364 35.71 - 53.57: 89 53.57 - 71.42: 9 71.42 - 89.28: 7 Dihedral angle restraints: 7127 sinusoidal: 2450 harmonic: 4677 Sorted by residual: dihedral pdb=" CB CYS N 193 " pdb=" SG CYS N 193 " pdb=" SG CYS S 97 " pdb=" CB CYS S 97 " ideal model delta sinusoidal sigma weight residual 93.00 137.83 -44.83 1 1.00e+01 1.00e-02 2.79e+01 dihedral pdb=" CA ILE B 488 " pdb=" C ILE B 488 " pdb=" N VAL B 489 " pdb=" CA VAL B 489 " ideal model delta harmonic sigma weight residual 180.00 154.93 25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA ASN B 62 " pdb=" C ASN B 62 " pdb=" N LEU B 63 " pdb=" CA LEU B 63 " ideal model delta harmonic sigma weight residual -180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 7124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1360 0.039 - 0.077: 479 0.077 - 0.116: 109 0.116 - 0.155: 20 0.155 - 0.193: 1 Chirality restraints: 1969 Sorted by residual: chirality pdb=" CB VAL A 555 " pdb=" CA VAL A 555 " pdb=" CG1 VAL A 555 " pdb=" CG2 VAL A 555 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA ASN B 200 " pdb=" N ASN B 200 " pdb=" C ASN B 200 " pdb=" CB ASN B 200 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA THR B 245 " pdb=" N THR B 245 " pdb=" C THR B 245 " pdb=" CB THR B 245 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 1966 not shown) Planarity restraints: 2071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 285 " 0.044 5.00e-02 4.00e+02 6.58e-02 6.92e+00 pdb=" N PRO B 286 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 286 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 286 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 576 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO B 577 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 577 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 577 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS N 196 " 0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO N 197 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO N 197 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO N 197 " 0.028 5.00e-02 4.00e+02 ... (remaining 2068 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3690 2.82 - 3.34: 10608 3.34 - 3.86: 19388 3.86 - 4.38: 20741 4.38 - 4.90: 36282 Nonbonded interactions: 90709 Sorted by model distance: nonbonded pdb=" O SER A 234 " pdb=" OG1 THR A 238 " model vdw 2.304 3.040 nonbonded pdb=" O VAL A 204 " pdb=" OG1 THR A 208 " model vdw 2.305 3.040 nonbonded pdb=" OD2 ASP A 382 " pdb=" OG SER A 384 " model vdw 2.317 3.040 nonbonded pdb=" O HIS S 36 " pdb=" OG1 THR S 40 " model vdw 2.320 3.040 nonbonded pdb=" O TYR A 478 " pdb=" OG1 THR A 482 " model vdw 2.320 3.040 ... (remaining 90704 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.290 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 : 0.003 0.049 11873 Z= 0.157 Angle : 0.613 11.446 16230 Z= 0.349 Chirality : 0.041 0.193 1969 Planarity : 0.006 0.066 2071 Dihedral : 12.403 89.277 4076 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.31 % Allowed : 9.78 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.98 (0.15), residues: 1561 helix: -2.32 (0.11), residues: 978 sheet: -1.54 (0.67), residues: 54 loop : -3.10 (0.22), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 24 TYR 0.011 0.001 TYR B 405 PHE 0.019 0.002 PHE B 492 TRP 0.023 0.002 TRP A 462 HIS 0.005 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00324 (11872) covalent geometry : angle 0.61303 (16228) SS BOND : bond 0.00310 ( 1) SS BOND : angle 1.74058 ( 2) hydrogen bonds : bond 0.06908 ( 677) hydrogen bonds : angle 4.90054 ( 2001) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 332 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8306 (m-80) cc_final: 0.8039 (m-10) REVERT: A 409 MET cc_start: 0.9127 (mmt) cc_final: 0.8535 (mmt) REVERT: B 139 LYS cc_start: 0.7987 (tppp) cc_final: 0.7782 (tppp) REVERT: B 140 THR cc_start: 0.8391 (p) cc_final: 0.8096 (t) REVERT: B 312 LYS cc_start: 0.8626 (tptt) cc_final: 0.7754 (mttt) REVERT: B 527 TRP cc_start: 0.8049 (t60) cc_final: 0.7005 (t60) REVERT: B 558 THR cc_start: 0.8304 (p) cc_final: 0.8034 (t) REVERT: M 18 ARG cc_start: 0.8030 (tpp80) cc_final: 0.7712 (mtp85) REVERT: M 60 ARG cc_start: 0.7044 (mmm160) cc_final: 0.6795 (mmm160) REVERT: M 93 PHE cc_start: 0.7072 (p90) cc_final: 0.6832 (p90) REVERT: M 100 ASN cc_start: 0.8371 (m110) cc_final: 0.8041 (m110) REVERT: M 122 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7501 (mm-40) REVERT: N 157 GLN cc_start: 0.8094 (tt0) cc_final: 0.7772 (tt0) REVERT: N 209 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7356 (mt-10) REVERT: N 223 TYR cc_start: 0.6687 (OUTLIER) cc_final: 0.4041 (t80) REVERT: S 9 ASN cc_start: 0.7818 (p0) cc_final: 0.7367 (p0) REVERT: S 61 ARG cc_start: 0.8355 (ttt-90) cc_final: 0.6812 (ptm-80) REVERT: S 122 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7784 (mp0) outliers start: 26 outliers final: 8 residues processed: 350 average time/residue: 0.1233 time to fit residues: 59.5212 Evaluate side-chains 223 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 214 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 581 PHE Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain N residue 223 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 216 GLN A 333 GLN A 387 GLN A 488 GLN ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 GLN B 278 ASN B 504 GLN B 505 GLN M 35 ASN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 121 HIS ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 202 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.159603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.128014 restraints weight = 20031.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.131264 restraints weight = 13384.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.133597 restraints weight = 10041.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.135264 restraints weight = 8185.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.136241 restraints weight = 7047.750| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11873 Z= 0.121 Angle : 0.578 8.170 16230 Z= 0.292 Chirality : 0.041 0.216 1969 Planarity : 0.004 0.047 2071 Dihedral : 5.276 59.553 1701 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.84 % Allowed : 15.91 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.20), residues: 1561 helix: -0.37 (0.15), residues: 988 sheet: -1.07 (0.68), residues: 54 loop : -2.60 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 21 TYR 0.022 0.001 TYR A 88 PHE 0.027 0.001 PHE B 492 TRP 0.016 0.002 TRP S 19 HIS 0.007 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00271 (11872) covalent geometry : angle 0.57776 (16228) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.83925 ( 2) hydrogen bonds : bond 0.03085 ( 677) hydrogen bonds : angle 4.04754 ( 2001) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8032 (m-80) cc_final: 0.7727 (m-80) REVERT: A 409 MET cc_start: 0.9020 (mmt) cc_final: 0.8415 (mmt) REVERT: A 474 ASP cc_start: 0.7222 (m-30) cc_final: 0.6901 (m-30) REVERT: A 602 MET cc_start: 0.7402 (mmp) cc_final: 0.7059 (mmm) REVERT: B 139 LYS cc_start: 0.8203 (tppp) cc_final: 0.7980 (tppt) REVERT: B 140 THR cc_start: 0.8148 (p) cc_final: 0.7943 (t) REVERT: B 312 LYS cc_start: 0.8488 (tptt) cc_final: 0.7878 (mttt) REVERT: B 527 TRP cc_start: 0.7771 (t60) cc_final: 0.6782 (t60) REVERT: B 558 THR cc_start: 0.8165 (p) cc_final: 0.7935 (t) REVERT: B 562 GLU cc_start: 0.7187 (tp30) cc_final: 0.6815 (tp30) REVERT: M 60 ARG cc_start: 0.7092 (mmm160) cc_final: 0.6650 (mmm-85) REVERT: M 84 LYS cc_start: 0.8331 (tmtt) cc_final: 0.8089 (tppp) REVERT: N 24 ARG cc_start: 0.7564 (mtm110) cc_final: 0.7346 (mtm-85) REVERT: N 185 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7703 (tp30) REVERT: N 223 TYR cc_start: 0.5835 (OUTLIER) cc_final: 0.3390 (t80) REVERT: S 9 ASN cc_start: 0.7701 (p0) cc_final: 0.7471 (p0) REVERT: S 61 ARG cc_start: 0.8220 (ttt-90) cc_final: 0.6851 (ptm-80) REVERT: S 122 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7615 (mm-30) REVERT: S 124 ARG cc_start: 0.7727 (ttt-90) cc_final: 0.7526 (ttp80) outliers start: 32 outliers final: 17 residues processed: 271 average time/residue: 0.1152 time to fit residues: 43.7977 Evaluate side-chains 223 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 581 PHE Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 108 ILE Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 213 TRP Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain S residue 126 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 58 optimal weight: 0.5980 chunk 149 optimal weight: 0.0020 chunk 33 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN ** N 192 HIS ** 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 = 0.4013 r_free = 0.4013 target = 0.159822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.128145 restraints weight = 20175.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.131493 restraints weight = 13447.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.133865 restraints weight = 10050.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.135326 restraints weight = 8158.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.136632 restraints weight = 7076.063| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11873 Z= 0.118 Angle : 0.565 10.197 16230 Z= 0.284 Chirality : 0.041 0.301 1969 Planarity : 0.004 0.053 2071 Dihedral : 5.063 53.075 1700 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.38 % Allowed : 17.24 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.21), residues: 1561 helix: 0.37 (0.16), residues: 990 sheet: -0.55 (0.72), residues: 54 loop : -2.39 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 304 TYR 0.016 0.001 TYR A 88 PHE 0.023 0.001 PHE B 492 TRP 0.015 0.001 TRP A 462 HIS 0.004 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00272 (11872) covalent geometry : angle 0.56509 (16228) SS BOND : bond 0.00006 ( 1) SS BOND : angle 0.52920 ( 2) hydrogen bonds : bond 0.03095 ( 677) hydrogen bonds : angle 3.97633 ( 2001) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8061 (m-80) cc_final: 0.7582 (m-80) REVERT: A 409 MET cc_start: 0.9004 (mmt) cc_final: 0.8451 (mmt) REVERT: A 602 MET cc_start: 0.7507 (mmp) cc_final: 0.7235 (mmm) REVERT: B 140 THR cc_start: 0.8224 (p) cc_final: 0.7987 (t) REVERT: B 527 TRP cc_start: 0.7809 (t60) cc_final: 0.6735 (t60) REVERT: B 558 THR cc_start: 0.8187 (p) cc_final: 0.7952 (t) REVERT: B 562 GLU cc_start: 0.7215 (tp30) cc_final: 0.6840 (tp30) REVERT: M 60 ARG cc_start: 0.7045 (mmm160) cc_final: 0.6646 (mmm-85) REVERT: M 77 MET cc_start: 0.7662 (ttp) cc_final: 0.7324 (ttt) REVERT: M 84 LYS cc_start: 0.8294 (tmtt) cc_final: 0.8053 (tppp) REVERT: N 185 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7712 (tp30) REVERT: N 223 TYR cc_start: 0.5663 (OUTLIER) cc_final: 0.3094 (t80) REVERT: S 61 ARG cc_start: 0.8176 (ttt-90) cc_final: 0.6790 (ptm-80) REVERT: S 122 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7599 (mp0) outliers start: 38 outliers final: 21 residues processed: 244 average time/residue: 0.1069 time to fit residues: 37.6448 Evaluate side-chains 218 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 581 PHE Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain N residue 158 ASN Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain S residue 38 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 86 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS A 522 GLN A 527 HIS A 531 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.157294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126620 restraints weight = 20357.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.127948 restraints weight = 14849.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.129515 restraints weight = 11306.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.130793 restraints weight = 9589.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.130943 restraints weight = 8897.050| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11873 Z= 0.153 Angle : 0.596 10.055 16230 Z= 0.298 Chirality : 0.042 0.272 1969 Planarity : 0.004 0.043 2071 Dihedral : 5.020 49.946 1700 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.56 % Allowed : 17.51 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.22), residues: 1561 helix: 0.79 (0.17), residues: 989 sheet: -0.36 (0.73), residues: 54 loop : -2.15 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG S 15 TYR 0.015 0.001 TYR S 20 PHE 0.022 0.002 PHE M 93 TRP 0.024 0.002 TRP N 173 HIS 0.006 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00360 (11872) covalent geometry : angle 0.59560 (16228) SS BOND : bond 0.00220 ( 1) SS BOND : angle 0.42282 ( 2) hydrogen bonds : bond 0.03246 ( 677) hydrogen bonds : angle 4.04547 ( 2001) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8138 (m-80) cc_final: 0.7871 (m-10) REVERT: A 353 MET cc_start: 0.5547 (ttt) cc_final: 0.5210 (ttt) REVERT: A 409 MET cc_start: 0.9069 (mmt) cc_final: 0.8544 (mmt) REVERT: A 602 MET cc_start: 0.7803 (mmp) cc_final: 0.7586 (mmm) REVERT: B 140 THR cc_start: 0.8367 (p) cc_final: 0.8138 (t) REVERT: B 527 TRP cc_start: 0.7906 (t60) cc_final: 0.6760 (t60) REVERT: M 84 LYS cc_start: 0.8264 (tmtt) cc_final: 0.8026 (tppp) REVERT: N 223 TYR cc_start: 0.6080 (OUTLIER) cc_final: 0.3459 (t80) REVERT: S 61 ARG cc_start: 0.8199 (ttt-90) cc_final: 0.6789 (ptm-80) REVERT: S 138 LEU cc_start: 0.8992 (mt) cc_final: 0.8787 (mt) outliers start: 40 outliers final: 33 residues processed: 237 average time/residue: 0.1078 time to fit residues: 37.1037 Evaluate side-chains 227 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 581 PHE Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 158 ASN Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 126 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 126 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 102 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.155595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.122929 restraints weight = 20404.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.126064 restraints weight = 14197.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.128141 restraints weight = 10868.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.129662 restraints weight = 9042.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.130598 restraints weight = 7916.635| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11873 Z= 0.177 Angle : 0.630 16.571 16230 Z= 0.312 Chirality : 0.042 0.278 1969 Planarity : 0.004 0.043 2071 Dihedral : 5.026 51.510 1698 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.18 % Allowed : 18.84 % Favored : 76.98 % 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 are not related in a simple way. whole: -0.12 (0.22), residues: 1561 helix: 0.93 (0.17), residues: 995 sheet: -0.41 (0.74), residues: 54 loop : -2.07 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 15 TYR 0.013 0.001 TYR B 300 PHE 0.019 0.002 PHE B 492 TRP 0.018 0.002 TRP N 213 HIS 0.006 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00423 (11872) covalent geometry : angle 0.63047 (16228) SS BOND : bond 0.00264 ( 1) SS BOND : angle 0.49544 ( 2) hydrogen bonds : bond 0.03350 ( 677) hydrogen bonds : angle 4.13617 ( 2001) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 198 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 TYR cc_start: 0.8318 (t80) cc_final: 0.7863 (t80) REVERT: A 353 MET cc_start: 0.5793 (ttt) cc_final: 0.5526 (ttt) REVERT: A 396 MET cc_start: 0.7117 (tpp) cc_final: 0.6672 (tpp) REVERT: A 409 MET cc_start: 0.9024 (mmt) cc_final: 0.8506 (mmt) REVERT: A 418 TYR cc_start: 0.7232 (m-80) cc_final: 0.7019 (m-10) REVERT: B 140 THR cc_start: 0.8245 (p) cc_final: 0.8044 (t) REVERT: B 527 TRP cc_start: 0.7890 (t60) cc_final: 0.6722 (t60) REVERT: B 528 ARG cc_start: 0.7393 (mtt180) cc_final: 0.7076 (mtm-85) REVERT: M 70 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8328 (mttp) REVERT: M 77 MET cc_start: 0.7710 (ttp) cc_final: 0.7347 (ttt) REVERT: M 84 LYS cc_start: 0.8380 (tmtt) cc_final: 0.8131 (tppp) REVERT: N 223 TYR cc_start: 0.5708 (OUTLIER) cc_final: 0.3147 (t80) REVERT: S 61 ARG cc_start: 0.8217 (ttt-90) cc_final: 0.6833 (ptm-80) REVERT: S 138 LEU cc_start: 0.8875 (mt) cc_final: 0.8567 (mt) outliers start: 47 outliers final: 33 residues processed: 229 average time/residue: 0.1047 time to fit residues: 34.8877 Evaluate side-chains 225 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 581 PHE Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 70 LYS Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 158 ASN Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 213 TRP Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain S residue 38 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 45 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.156181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125787 restraints weight = 20279.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.127193 restraints weight = 14408.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.128647 restraints weight = 10947.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.129579 restraints weight = 9593.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.129788 restraints weight = 8966.471| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11873 Z= 0.155 Angle : 0.608 11.997 16230 Z= 0.301 Chirality : 0.042 0.273 1969 Planarity : 0.004 0.042 2071 Dihedral : 4.949 51.572 1696 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.64 % Allowed : 20.18 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.22), residues: 1561 helix: 1.05 (0.17), residues: 996 sheet: -0.46 (0.74), residues: 54 loop : -2.06 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 15 TYR 0.011 0.001 TYR A 502 PHE 0.033 0.002 PHE A 66 TRP 0.019 0.002 TRP N 207 HIS 0.005 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00365 (11872) covalent geometry : angle 0.60765 (16228) SS BOND : bond 0.00209 ( 1) SS BOND : angle 0.45348 ( 2) hydrogen bonds : bond 0.03274 ( 677) hydrogen bonds : angle 4.08377 ( 2001) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 MET cc_start: 0.7229 (tpp) cc_final: 0.6740 (tpp) REVERT: A 409 MET cc_start: 0.9033 (mmt) cc_final: 0.8513 (mmt) REVERT: B 140 THR cc_start: 0.8282 (p) cc_final: 0.8039 (t) REVERT: B 527 TRP cc_start: 0.7884 (t60) cc_final: 0.6721 (t60) REVERT: M 77 MET cc_start: 0.7738 (ttp) cc_final: 0.7437 (ttt) REVERT: M 84 LYS cc_start: 0.8300 (tmtt) cc_final: 0.8037 (tppp) REVERT: M 93 PHE cc_start: 0.7538 (p90) cc_final: 0.6797 (p90) REVERT: N 223 TYR cc_start: 0.6061 (OUTLIER) cc_final: 0.3465 (t80) REVERT: S 61 ARG cc_start: 0.8248 (ttt-90) cc_final: 0.6750 (ptm-80) REVERT: S 89 GLU cc_start: 0.7632 (tt0) cc_final: 0.7305 (tt0) REVERT: S 122 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7263 (mm-30) outliers start: 41 outliers final: 29 residues processed: 230 average time/residue: 0.1093 time to fit residues: 36.6203 Evaluate side-chains 225 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 581 PHE Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain S residue 38 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 73 optimal weight: 0.5980 chunk 11 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.156172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.126572 restraints weight = 20409.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126736 restraints weight = 14242.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.128778 restraints weight = 11593.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.130571 restraints weight = 9260.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.130743 restraints weight = 8004.875| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11873 Z= 0.134 Angle : 0.597 12.967 16230 Z= 0.297 Chirality : 0.041 0.277 1969 Planarity : 0.003 0.042 2071 Dihedral : 4.965 54.835 1696 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.64 % Allowed : 21.16 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.22), residues: 1561 helix: 1.12 (0.17), residues: 995 sheet: -0.45 (0.76), residues: 54 loop : -2.02 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 421 TYR 0.020 0.001 TYR A 418 PHE 0.017 0.001 PHE B 492 TRP 0.019 0.002 TRP A 462 HIS 0.004 0.001 HIS N 192 Details of bonding type rmsd covalent geometry : bond 0.00317 (11872) covalent geometry : angle 0.59743 (16228) SS BOND : bond 0.00128 ( 1) SS BOND : angle 0.40178 ( 2) hydrogen bonds : bond 0.03237 ( 677) hydrogen bonds : angle 4.04613 ( 2001) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 MET cc_start: 0.7208 (tpp) cc_final: 0.6703 (tpp) REVERT: A 409 MET cc_start: 0.9099 (mmt) cc_final: 0.8560 (mmt) REVERT: B 140 THR cc_start: 0.8221 (p) cc_final: 0.8018 (t) REVERT: B 448 MET cc_start: 0.8419 (tpt) cc_final: 0.7765 (tpt) REVERT: B 527 TRP cc_start: 0.7902 (t60) cc_final: 0.6743 (t60) REVERT: M 84 LYS cc_start: 0.8237 (tmtt) cc_final: 0.7949 (tppp) REVERT: M 122 GLN cc_start: 0.7987 (mm110) cc_final: 0.7762 (mm110) REVERT: N 223 TYR cc_start: 0.5985 (OUTLIER) cc_final: 0.3374 (t80) REVERT: S 61 ARG cc_start: 0.8265 (ttt-90) cc_final: 0.6734 (ptm-80) REVERT: S 89 GLU cc_start: 0.7713 (tt0) cc_final: 0.7365 (tt0) REVERT: S 122 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7467 (mp0) outliers start: 41 outliers final: 29 residues processed: 235 average time/residue: 0.1004 time to fit residues: 34.4558 Evaluate side-chains 224 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 581 PHE Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain S residue 38 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 108 optimal weight: 5.9990 chunk 136 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 57 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 123 optimal weight: 0.4980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 192 HIS ** 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 = 0.3946 r_free = 0.3946 target = 0.153961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.124308 restraints weight = 20725.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.123946 restraints weight = 14321.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.125655 restraints weight = 11880.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.127271 restraints weight = 9899.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.127369 restraints weight = 9254.720| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11873 Z= 0.160 Angle : 0.634 15.134 16230 Z= 0.311 Chirality : 0.042 0.322 1969 Planarity : 0.004 0.042 2071 Dihedral : 4.999 52.788 1696 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.29 % Allowed : 21.60 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.22), residues: 1561 helix: 1.10 (0.17), residues: 996 sheet: -0.49 (0.77), residues: 54 loop : -1.94 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 15 TYR 0.026 0.001 TYR A 88 PHE 0.033 0.002 PHE A 66 TRP 0.037 0.002 TRP N 213 HIS 0.006 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00377 (11872) covalent geometry : angle 0.63411 (16228) SS BOND : bond 0.00214 ( 1) SS BOND : angle 0.35378 ( 2) hydrogen bonds : bond 0.03318 ( 677) hydrogen bonds : angle 4.12214 ( 2001) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 GLN cc_start: 0.7970 (pt0) cc_final: 0.7510 (mt0) REVERT: A 396 MET cc_start: 0.7216 (tpp) cc_final: 0.6722 (tpp) REVERT: A 409 MET cc_start: 0.9105 (mmt) cc_final: 0.8564 (mmt) REVERT: B 448 MET cc_start: 0.8534 (tpt) cc_final: 0.7664 (tpt) REVERT: B 527 TRP cc_start: 0.7920 (t60) cc_final: 0.6686 (t60) REVERT: M 84 LYS cc_start: 0.8264 (tmtt) cc_final: 0.7979 (tppp) REVERT: N 195 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8520 (m) REVERT: N 223 TYR cc_start: 0.6008 (OUTLIER) cc_final: 0.3393 (t80) REVERT: S 21 MET cc_start: 0.7221 (mmm) cc_final: 0.6994 (mmm) REVERT: S 61 ARG cc_start: 0.8258 (ttt-90) cc_final: 0.6743 (ptm-80) REVERT: S 89 GLU cc_start: 0.7654 (tt0) cc_final: 0.7318 (tt0) REVERT: S 122 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7274 (mm-30) outliers start: 37 outliers final: 29 residues processed: 222 average time/residue: 0.1026 time to fit residues: 33.6655 Evaluate side-chains 224 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 581 PHE Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 195 VAL Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain S residue 38 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 123 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 94 optimal weight: 0.3980 chunk 101 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.157191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.127183 restraints weight = 20125.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.129212 restraints weight = 14131.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.130918 restraints weight = 10602.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132026 restraints weight = 8873.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.132218 restraints weight = 8161.477| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11873 Z= 0.129 Angle : 0.611 13.420 16230 Z= 0.300 Chirality : 0.042 0.312 1969 Planarity : 0.003 0.042 2071 Dihedral : 4.899 49.287 1696 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.02 % Allowed : 22.76 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.22), residues: 1561 helix: 1.16 (0.17), residues: 994 sheet: -0.44 (0.76), residues: 54 loop : -1.87 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 390 TYR 0.017 0.001 TYR B 277 PHE 0.018 0.001 PHE M 93 TRP 0.022 0.002 TRP N 213 HIS 0.004 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00303 (11872) covalent geometry : angle 0.61062 (16228) SS BOND : bond 0.00095 ( 1) SS BOND : angle 0.40131 ( 2) hydrogen bonds : bond 0.03188 ( 677) hydrogen bonds : angle 4.07713 ( 2001) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8212 (m-80) cc_final: 0.7957 (m-10) REVERT: A 166 GLN cc_start: 0.7973 (pt0) cc_final: 0.7473 (mt0) REVERT: A 396 MET cc_start: 0.7211 (tpp) cc_final: 0.6727 (tpp) REVERT: A 409 MET cc_start: 0.9121 (mmt) cc_final: 0.8541 (mmt) REVERT: A 504 LEU cc_start: 0.8299 (mt) cc_final: 0.8026 (mt) REVERT: A 551 LEU cc_start: 0.7167 (tp) cc_final: 0.6863 (tp) REVERT: B 448 MET cc_start: 0.8516 (tpt) cc_final: 0.7616 (tpt) REVERT: B 527 TRP cc_start: 0.7862 (t60) cc_final: 0.6736 (t60) REVERT: M 84 LYS cc_start: 0.8254 (tmtt) cc_final: 0.7948 (tppp) REVERT: T 7 ASP cc_start: 0.6842 (t70) cc_final: 0.6226 (t70) REVERT: N 195 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8488 (m) REVERT: N 219 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8037 (mm) REVERT: N 223 TYR cc_start: 0.5990 (OUTLIER) cc_final: 0.3989 (t80) REVERT: S 61 ARG cc_start: 0.8233 (ttt-90) cc_final: 0.6686 (ptm-80) REVERT: S 89 GLU cc_start: 0.7697 (tt0) cc_final: 0.7332 (tt0) REVERT: S 122 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7499 (mm-30) outliers start: 34 outliers final: 31 residues processed: 226 average time/residue: 0.1053 time to fit residues: 34.8880 Evaluate side-chains 228 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 581 PHE Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 195 VAL Chi-restraints excluded: chain N residue 213 TRP Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain S residue 38 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 137 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 106 optimal weight: 0.3980 chunk 89 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 192 HIS ** 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 = 0.3994 r_free = 0.3994 target = 0.157966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.128006 restraints weight = 20258.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.130001 restraints weight = 13837.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.131575 restraints weight = 10369.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.132798 restraints weight = 8678.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.132995 restraints weight = 8147.182| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11873 Z= 0.130 Angle : 0.640 13.754 16230 Z= 0.310 Chirality : 0.042 0.300 1969 Planarity : 0.004 0.042 2071 Dihedral : 4.863 52.346 1696 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.29 % Allowed : 22.31 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.22), residues: 1561 helix: 1.17 (0.17), residues: 996 sheet: -0.42 (0.75), residues: 54 loop : -1.84 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 390 TYR 0.016 0.001 TYR B 277 PHE 0.035 0.002 PHE A 66 TRP 0.022 0.002 TRP N 213 HIS 0.006 0.001 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00305 (11872) covalent geometry : angle 0.64015 (16228) SS BOND : bond 0.00082 ( 1) SS BOND : angle 0.41755 ( 2) hydrogen bonds : bond 0.03175 ( 677) hydrogen bonds : angle 4.11535 ( 2001) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 GLN cc_start: 0.7964 (pt0) cc_final: 0.7487 (mt0) REVERT: A 396 MET cc_start: 0.7193 (tpp) cc_final: 0.6690 (tpp) REVERT: A 409 MET cc_start: 0.9114 (mmt) cc_final: 0.8539 (mmt) REVERT: A 504 LEU cc_start: 0.8288 (mt) cc_final: 0.8036 (mt) REVERT: A 551 LEU cc_start: 0.7241 (tp) cc_final: 0.6935 (tp) REVERT: B 411 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8460 (tt) REVERT: B 448 MET cc_start: 0.8509 (tpt) cc_final: 0.7593 (tpt) REVERT: B 527 TRP cc_start: 0.7825 (t60) cc_final: 0.6632 (t60) REVERT: B 562 GLU cc_start: 0.7225 (tp30) cc_final: 0.6999 (tt0) REVERT: M 77 MET cc_start: 0.7473 (ttt) cc_final: 0.7090 (ttt) REVERT: M 84 LYS cc_start: 0.8290 (tmtt) cc_final: 0.7989 (tppp) REVERT: T 7 ASP cc_start: 0.6794 (t70) cc_final: 0.6174 (t70) REVERT: N 195 VAL cc_start: 0.8848 (OUTLIER) cc_final: 0.8459 (m) REVERT: N 223 TYR cc_start: 0.6561 (OUTLIER) cc_final: 0.3832 (t80) REVERT: S 61 ARG cc_start: 0.8230 (ttt-90) cc_final: 0.6686 (ptm-80) REVERT: S 89 GLU cc_start: 0.7689 (tt0) cc_final: 0.7332 (tt0) REVERT: S 122 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7495 (mp0) outliers start: 37 outliers final: 31 residues processed: 218 average time/residue: 0.1024 time to fit residues: 33.3592 Evaluate side-chains 223 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 581 PHE Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 195 VAL Chi-restraints excluded: chain N residue 213 TRP Chi-restraints excluded: chain N residue 223 TYR Chi-restraints excluded: chain S residue 38 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 129 optimal weight: 0.8980 chunk 153 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.158296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.128651 restraints weight = 20259.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.129886 restraints weight = 14363.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.131697 restraints weight = 10768.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.133201 restraints weight = 9015.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.133213 restraints weight = 7919.343| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11873 Z= 0.136 Angle : 0.636 13.759 16230 Z= 0.311 Chirality : 0.042 0.307 1969 Planarity : 0.004 0.042 2071 Dihedral : 4.890 55.413 1696 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.11 % Allowed : 22.58 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.22), residues: 1561 helix: 1.21 (0.17), residues: 994 sheet: -0.49 (0.75), residues: 54 loop : -1.81 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 390 TYR 0.020 0.001 TYR M 83 PHE 0.018 0.001 PHE M 93 TRP 0.020 0.002 TRP N 213 HIS 0.005 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00324 (11872) covalent geometry : angle 0.63590 (16228) SS BOND : bond 0.00104 ( 1) SS BOND : angle 0.49100 ( 2) hydrogen bonds : bond 0.03174 ( 677) hydrogen bonds : angle 4.09188 ( 2001) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1872.92 seconds wall clock time: 33 minutes 12.12 seconds (1992.12 seconds total)