Starting phenix.real_space_refine on Sat Mar 7 13:18:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kw7_23050/03_2026/7kw7_23050_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kw7_23050/03_2026/7kw7_23050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kw7_23050/03_2026/7kw7_23050_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kw7_23050/03_2026/7kw7_23050_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kw7_23050/03_2026/7kw7_23050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kw7_23050/03_2026/7kw7_23050.map" } resolution = 3.57 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= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 Mg 2 5.21 5 S 101 5.16 5 C 13803 2.51 5 N 3723 2.21 5 O 4217 1.98 5 H 21928 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 107 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: 43780 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 10157 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 15, 'TRANS': 607} Chain breaks: 1 Chain: "B" Number of atoms: 10233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 10233 Classifications: {'peptide': 628} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 611} Chain breaks: 2 Chain: "C" Number of atoms: 7897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 7897 Classifications: {'peptide': 511} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 489} Chain breaks: 1 Chain: "D" Number of atoms: 5882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 5882 Classifications: {'peptide': 379} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 365} Chain: "E" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5321 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain: "F" Number of atoms: 4232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 4232 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 247} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.83, per 1000 atoms: 0.18 Number of scatterers: 43780 At special positions: 0 Unit cell: (145.083, 154.614, 130.257, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) K 2 19.00 S 101 16.00 P 4 15.00 Mg 2 11.99 O 4217 8.00 N 3723 7.00 C 13803 6.00 H 21928 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.22 Conformation dependent library (CDL) restraints added in 1.2 seconds 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5166 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 23 sheets defined 55.6% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 23 through 36 Processing helix chain 'A' and resid 42 through 63 Processing helix chain 'A' and resid 64 through 65 No H-bonds generated for 'chain 'A' and resid 64 through 65' Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 99 through 105 Processing helix chain 'A' and resid 106 through 109 Processing helix chain 'A' and resid 110 through 124 Processing helix chain 'A' and resid 127 through 135 removed outlier: 4.408A pdb=" N GLY A 132 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 143 Processing helix chain 'A' and resid 192 through 198 removed outlier: 5.199A pdb=" N GLU A 196 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 295 through 299 Processing helix chain 'A' and resid 305 through 318 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 356 through 359 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 399 through 405 Processing helix chain 'A' and resid 406 through 429 Processing helix chain 'A' and resid 430 through 452 removed outlier: 4.371A pdb=" N LYS A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASN A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 461 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 498 through 504 Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 508 through 514 Processing helix chain 'A' and resid 525 through 533 removed outlier: 4.366A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 568 Processing helix chain 'A' and resid 568 through 579 Processing helix chain 'A' and resid 607 through 618 Processing helix chain 'A' and resid 622 through 630 Processing helix chain 'A' and resid 640 through 653 Processing helix chain 'A' and resid 656 through 674 Processing helix chain 'A' and resid 680 through 696 Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 42 through 66 removed outlier: 3.572A pdb=" N LEU B 64 " --> pdb=" O ARG B 60 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR B 65 " --> pdb=" O TYR B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 99 through 105 Processing helix chain 'B' and resid 106 through 109 removed outlier: 3.681A pdb=" N THR B 109 " --> pdb=" O ASN B 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 106 through 109' Processing helix chain 'B' and resid 110 through 124 removed outlier: 5.277A pdb=" N LYS B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 135 removed outlier: 4.323A pdb=" N GLY B 132 " --> pdb=" O SER B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 143 Processing helix chain 'B' and resid 192 through 198 removed outlier: 4.893A pdb=" N GLU B 196 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 305 through 318 Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 399 through 405 Processing helix chain 'B' and resid 406 through 430 removed outlier: 3.723A pdb=" N ASP B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 452 removed outlier: 3.502A pdb=" N LYS B 436 " --> pdb=" O GLU B 432 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ASN B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 461 Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 498 through 504 Processing helix chain 'B' and resid 505 through 507 No H-bonds generated for 'chain 'B' and resid 505 through 507' Processing helix chain 'B' and resid 508 through 514 Processing helix chain 'B' and resid 525 through 533 removed outlier: 4.355A pdb=" N GLN B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 568 Processing helix chain 'B' and resid 568 through 579 Processing helix chain 'B' and resid 607 through 621 Processing helix chain 'B' and resid 640 through 653 Processing helix chain 'B' and resid 656 through 674 Processing helix chain 'B' and resid 680 through 697 Processing helix chain 'C' and resid 52 through 57 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 80 through 88 removed outlier: 3.539A pdb=" N LYS C 88 " --> pdb=" O GLN C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 136 Processing helix chain 'C' and resid 151 through 165 Processing helix chain 'C' and resid 175 through 183 Processing helix chain 'C' and resid 229 through 250 removed outlier: 3.755A pdb=" N PHE C 233 " --> pdb=" O GLY C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 255 Processing helix chain 'C' and resid 256 through 277 removed outlier: 3.954A pdb=" N SER C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 306 Processing helix chain 'C' and resid 306 through 312 Processing helix chain 'C' and resid 314 through 325 Processing helix chain 'C' and resid 327 through 331 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 343 through 354 Processing helix chain 'C' and resid 367 through 381 Processing helix chain 'C' and resid 388 through 395 Processing helix chain 'C' and resid 449 through 453 Processing helix chain 'C' and resid 635 through 639 Processing helix chain 'D' and resid 52 through 57 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 69 through 74 removed outlier: 3.982A pdb=" N LEU D 73 " --> pdb=" O ASP D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 87 Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 115 through 136 Processing helix chain 'D' and resid 151 through 166 Processing helix chain 'D' and resid 175 through 183 Processing helix chain 'D' and resid 230 through 250 Processing helix chain 'D' and resid 256 through 274 Processing helix chain 'D' and resid 299 through 306 Processing helix chain 'D' and resid 306 through 313 removed outlier: 3.637A pdb=" N THR D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 324 Processing helix chain 'D' and resid 338 through 342 Processing helix chain 'D' and resid 343 through 354 Processing helix chain 'D' and resid 367 through 381 Processing helix chain 'E' and resid 219 through 238 Processing helix chain 'E' and resid 240 through 255 Processing helix chain 'E' and resid 258 through 273 removed outlier: 4.412A pdb=" N ILE E 262 " --> pdb=" O ASN E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 292 Processing helix chain 'E' and resid 295 through 313 Processing helix chain 'E' and resid 315 through 330 Processing helix chain 'E' and resid 332 through 355 Processing helix chain 'E' and resid 356 through 372 Processing helix chain 'E' and resid 375 through 390 Processing helix chain 'E' and resid 393 through 407 Processing helix chain 'E' and resid 409 through 424 Processing helix chain 'E' and resid 427 through 441 removed outlier: 3.634A pdb=" N TYR E 431 " --> pdb=" O PHE E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 458 Processing helix chain 'E' and resid 461 through 478 removed outlier: 3.798A pdb=" N MET E 473 " --> pdb=" O GLN E 469 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N TYR E 476 " --> pdb=" O MET E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 481 through 490 removed outlier: 3.504A pdb=" N VAL E 485 " --> pdb=" O SER E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 501 Processing helix chain 'E' and resid 501 through 514 Processing helix chain 'E' and resid 514 through 522 removed outlier: 3.525A pdb=" N LEU E 518 " --> pdb=" O ASP E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 537 removed outlier: 4.210A pdb=" N LYS E 530 " --> pdb=" O VAL E 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 539 Processing helix chain 'F' and resid 558 through 580 removed outlier: 5.417A pdb=" N ASN F 564 " --> pdb=" O MET F 560 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 587 Processing helix chain 'F' and resid 588 through 617 removed outlier: 5.872A pdb=" N MET F 601 " --> pdb=" O GLN F 597 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER F 602 " --> pdb=" O TYR F 598 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER F 617 " --> pdb=" O TYR F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 636 through 657 removed outlier: 5.686A pdb=" N GLN F 642 " --> pdb=" O CYS F 638 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N HIS F 645 " --> pdb=" O ASP F 641 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET F 646 " --> pdb=" O GLN F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 659 through 672 removed outlier: 4.058A pdb=" N LEU F 672 " --> pdb=" O THR F 668 " (cutoff:3.500A) Processing helix chain 'F' and resid 682 through 706 removed outlier: 3.571A pdb=" N PHE F 686 " --> pdb=" O SER F 682 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG F 704 " --> pdb=" O ALA F 700 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY F 706 " --> pdb=" O VAL F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 708 through 742 removed outlier: 4.265A pdb=" N HIS F 726 " --> pdb=" O LEU F 722 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU F 727 " --> pdb=" O ASP F 723 " (cutoff:3.500A) Processing helix chain 'F' and resid 743 through 746 Processing helix chain 'F' and resid 750 through 765 Proline residue: F 762 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 21 removed outlier: 7.108A pdb=" N HIS A 189 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL A 148 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE A 187 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL A 150 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LYS A 185 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR A 152 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY A 183 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 368 through 371 removed outlier: 6.953A pdb=" N LEU A 363 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS A 362 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N SER A 391 " --> pdb=" O LYS A 362 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR A 364 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE A 337 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N SER A 330 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA A 339 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N HIS A 328 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU A 341 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL A 326 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 343 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 37.702A pdb=" N LEU A 324 " --> pdb=" O ASP C 225 " (cutoff:3.500A) removed outlier: 33.106A pdb=" N ASP C 225 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 26.279A pdb=" N VAL A 326 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 21.038A pdb=" N ALA C 223 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 16.332A pdb=" N HIS A 328 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 11.375A pdb=" N ALA C 221 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER A 330 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL C 219 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHE C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP C 213 " --> pdb=" O PHE C 217 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N VAL C 219 " --> pdb=" O THR C 211 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR C 211 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 476 removed outlier: 4.117A pdb=" N TYR A 466 " --> pdb=" O TYR A 520 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N ILE A 519 " --> pdb=" O HIS A 490 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TYR A 492 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N MET A 521 " --> pdb=" O TYR A 492 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE A 494 " --> pdb=" O MET A 521 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 585 through 588 removed outlier: 6.420A pdb=" N LYS A 585 " --> pdb=" O LEU A 634 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE A 636 " --> pdb=" O LYS A 585 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A 587 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 18 through 19 removed outlier: 3.521A pdb=" N LYS B 147 " --> pdb=" O HIS B 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 368 through 371 removed outlier: 6.778A pdb=" N LEU B 363 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHE B 337 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER B 330 " --> pdb=" O PHE B 337 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA B 339 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N HIS B 328 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B 341 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL B 326 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 343 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 35.467A pdb=" N LEU B 324 " --> pdb=" O ASP D 225 " (cutoff:3.500A) removed outlier: 30.573A pdb=" N ASP D 225 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 24.208A pdb=" N VAL B 326 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 18.982A pdb=" N ALA D 223 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 14.629A pdb=" N HIS B 328 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N ALA D 221 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N SER B 330 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL D 219 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N PHE D 217 " --> pdb=" O ASP D 213 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ASP D 213 " --> pdb=" O PHE D 217 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL D 219 " --> pdb=" O THR D 211 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR D 211 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN D 194 " --> pdb=" O ASP D 333 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL D 335 " --> pdb=" O ASN D 194 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU D 196 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL D 337 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N PHE D 198 " --> pdb=" O VAL D 337 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 475 through 476 removed outlier: 4.002A pdb=" N TYR B 466 " --> pdb=" O TYR B 520 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N ILE B 519 " --> pdb=" O HIS B 490 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TYR B 492 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N MET B 521 " --> pdb=" O TYR B 492 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 494 " --> pdb=" O MET B 521 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 585 through 588 removed outlier: 6.384A pdb=" N LYS B 585 " --> pdb=" O LEU B 634 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE B 636 " --> pdb=" O LYS B 585 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 587 " --> pdb=" O ILE B 636 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 28 Processing sheet with id=AB1, first strand: chain 'C' and resid 25 through 28 removed outlier: 4.346A pdb=" N LEU C 11 " --> pdb=" O THR C 145 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ALA C 142 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE C 172 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE C 144 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASN C 174 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N VAL C 146 " --> pdb=" O ASN C 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 49 through 51 Processing sheet with id=AB3, first strand: chain 'C' and resid 93 through 95 Processing sheet with id=AB4, first strand: chain 'C' and resid 279 through 288 removed outlier: 3.653A pdb=" N SER C 286 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE C 291 " --> pdb=" O SER C 286 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 409 through 414 removed outlier: 6.790A pdb=" N LEU C 401 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN C 441 " --> pdb=" O GLU C 404 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL C 438 " --> pdb=" O GLU C 460 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU C 460 " --> pdb=" O VAL C 438 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE C 440 " --> pdb=" O ARG C 458 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ARG C 458 " --> pdb=" O ILE C 440 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL C 442 " --> pdb=" O LEU C 456 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 498 through 503 Processing sheet with id=AB7, first strand: chain 'D' and resid 25 through 28 Processing sheet with id=AB8, first strand: chain 'D' and resid 25 through 28 removed outlier: 4.670A pdb=" N LEU D 11 " --> pdb=" O THR D 145 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ALA D 142 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE D 172 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE D 144 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ASN D 174 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL D 146 " --> pdb=" O ASN D 174 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 49 through 51 Processing sheet with id=AC1, first strand: chain 'D' and resid 93 through 96 removed outlier: 3.517A pdb=" N GLN D 93 " --> pdb=" O GLN D 104 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 279 through 288 removed outlier: 3.746A pdb=" N SER D 286 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ILE D 291 " --> pdb=" O SER D 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 541 through 542 Processing sheet with id=AC4, first strand: chain 'F' and resid 622 through 624 removed outlier: 3.530A pdb=" N ALA F 624 " --> pdb=" O LEU F 627 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 674 through 676 1256 hydrogen bonds defined for protein. 3483 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: 11.09 Time building geometry restraints manager: 5.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 21900 1.13 - 1.31: 4215 1.31 - 1.49: 9486 1.49 - 1.68: 8373 1.68 - 1.86: 167 Bond restraints: 44141 Sorted by residual: bond pdb=" CD GLU D 175 " pdb=" OE1 GLU D 175 " ideal model delta sigma weight residual 1.249 1.059 0.190 1.90e-02 2.77e+03 9.96e+01 bond pdb=" NE2 HIS D 240 " pdb=" HE2 HIS D 240 " ideal model delta sigma weight residual 0.860 1.059 -0.199 2.00e-02 2.50e+03 9.90e+01 bond pdb=" NE1 TRP B 297 " pdb=" HE1 TRP B 297 " ideal model delta sigma weight residual 0.860 1.054 -0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" NE2 HIS C 240 " pdb=" HE2 HIS C 240 " ideal model delta sigma weight residual 0.860 1.053 -0.193 2.00e-02 2.50e+03 9.32e+01 bond pdb=" CD GLU C 175 " pdb=" OE2 GLU C 175 " ideal model delta sigma weight residual 1.249 1.066 0.183 1.90e-02 2.77e+03 9.25e+01 ... (remaining 44136 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 71037 2.98 - 5.96: 6846 5.96 - 8.94: 1928 8.94 - 11.92: 122 11.92 - 14.90: 38 Bond angle restraints: 79971 Sorted by residual: angle pdb=" C ASN E 390 " pdb=" N PRO E 391 " pdb=" CA PRO E 391 " ideal model delta sigma weight residual 119.56 129.56 -10.00 1.02e+00 9.61e-01 9.62e+01 angle pdb=" C GLU E 424 " pdb=" N PRO E 425 " pdb=" CA PRO E 425 " ideal model delta sigma weight residual 119.56 127.52 -7.96 1.02e+00 9.61e-01 6.09e+01 angle pdb=" C VAL B 343 " pdb=" N PRO B 344 " pdb=" CA PRO B 344 " ideal model delta sigma weight residual 120.03 127.70 -7.67 9.90e-01 1.02e+00 6.00e+01 angle pdb=" C ILE A 59 " pdb=" CA ILE A 59 " pdb=" CB ILE A 59 " ideal model delta sigma weight residual 112.02 101.99 10.03 1.31e+00 5.83e-01 5.86e+01 angle pdb=" N ILE C 29 " pdb=" CA ILE C 29 " pdb=" C ILE C 29 " ideal model delta sigma weight residual 108.17 118.75 -10.58 1.40e+00 5.10e-01 5.71e+01 ... (remaining 79966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 20243 34.74 - 69.48: 307 69.48 - 104.22: 16 104.22 - 138.96: 3 138.96 - 173.70: 2 Dihedral angle restraints: 20571 sinusoidal: 11412 harmonic: 9159 Sorted by residual: dihedral pdb=" C5' ADP C 701 " pdb=" O5' ADP C 701 " pdb=" PA ADP C 701 " pdb=" O2A ADP C 701 " ideal model delta sinusoidal sigma weight residual 300.00 126.30 173.70 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP D 701 " pdb=" O3A ADP D 701 " pdb=" PA ADP D 701 " pdb=" PB ADP D 701 " ideal model delta sinusoidal sigma weight residual 300.00 156.14 143.86 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" O1B ADP D 701 " pdb=" O3A ADP D 701 " pdb=" PB ADP D 701 " pdb=" PA ADP D 701 " ideal model delta sinusoidal sigma weight residual -60.00 78.19 -138.20 1 2.00e+01 2.50e-03 4.19e+01 ... (remaining 20568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1930 0.075 - 0.150: 1004 0.150 - 0.225: 342 0.225 - 0.300: 67 0.300 - 0.375: 16 Chirality restraints: 3359 Sorted by residual: chirality pdb=" CB ILE A 285 " pdb=" CA ILE A 285 " pdb=" CG1 ILE A 285 " pdb=" CG2 ILE A 285 " both_signs ideal model delta sigma weight residual False 2.64 3.02 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA ASN B 360 " pdb=" N ASN B 360 " pdb=" C ASN B 360 " pdb=" CB ASN B 360 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CB VAL E 268 " pdb=" CA VAL E 268 " pdb=" CG1 VAL E 268 " pdb=" CG2 VAL E 268 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 3356 not shown) Planarity restraints: 6491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 732 " -0.029 2.00e-02 2.50e+03 5.89e-02 3.47e+01 pdb=" C ASP B 732 " 0.102 2.00e-02 2.50e+03 pdb=" O ASP B 732 " -0.037 2.00e-02 2.50e+03 pdb=" OXT ASP B 732 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 548 " 0.075 2.00e-02 2.50e+03 3.06e-02 2.80e+01 pdb=" CG TYR F 548 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR F 548 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR F 548 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR F 548 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR F 548 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR F 548 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR F 548 " 0.048 2.00e-02 2.50e+03 pdb=" HD1 TYR F 548 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR F 548 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR F 548 " 0.014 2.00e-02 2.50e+03 pdb=" HE2 TYR F 548 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 162 " 0.072 2.00e-02 2.50e+03 2.43e-02 2.35e+01 pdb=" CG TRP A 162 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TRP A 162 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 162 " -0.022 2.00e-02 2.50e+03 pdb=" NE1 TRP A 162 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP A 162 " -0.020 2.00e-02 2.50e+03 pdb=" CE3 TRP A 162 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 162 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 162 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 162 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP A 162 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 TRP A 162 " 0.025 2.00e-02 2.50e+03 pdb=" HE3 TRP A 162 " -0.010 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 162 " 0.018 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 162 " -0.007 2.00e-02 2.50e+03 pdb=" HH2 TRP A 162 " 0.025 2.00e-02 2.50e+03 ... (remaining 6488 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.95: 882 1.95 - 2.75: 82811 2.75 - 3.55: 176185 3.55 - 4.34: 271763 4.34 - 5.14: 438891 Nonbonded interactions: 970532 Sorted by model distance: nonbonded pdb=" H PHE A 384 " pdb=" H ILE A 385 " model vdw 1.156 2.100 nonbonded pdb=" H PHE B 384 " pdb=" H ILE B 385 " model vdw 1.163 2.100 nonbonded pdb=" H VAL C 388 " pdb=" H GLN C 389 " model vdw 1.234 2.100 nonbonded pdb=" H THR C 278 " pdb=" H GLN C 279 " model vdw 1.314 2.100 nonbonded pdb=" OD1 ASP C 10 " pdb=" K K C 703 " model vdw 1.517 2.730 ... (remaining 970527 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 16 through 699) } 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.260 Extract box with map and model: 0.510 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 41.080 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 : 0.021 0.194 22213 Z= 1.121 Angle : 1.733 13.555 29945 Z= 1.168 Chirality : 0.098 0.375 3359 Planarity : 0.009 0.059 3858 Dihedral : 11.040 173.701 8497 Min Nonbonded Distance : 1.517 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.26 % Favored : 98.71 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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: 0.61 (0.15), residues: 2707 helix: -0.13 (0.12), residues: 1335 sheet: 1.32 (0.26), residues: 378 loop : 1.16 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 704 TYR 0.069 0.009 TYR F 548 PHE 0.041 0.007 PHE D 150 TRP 0.047 0.011 TRP A 162 HIS 0.010 0.002 HIS C 240 Details of bonding type rmsd covalent geometry : bond 0.02107 (22213) covalent geometry : angle 1.73306 (29945) hydrogen bonds : bond 0.16314 ( 1248) hydrogen bonds : angle 6.96642 ( 3483) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.7273 (mtm) cc_final: 0.6963 (mtt) REVERT: A 614 MET cc_start: 0.8270 (mmm) cc_final: 0.8033 (mmm) REVERT: B 38 TYR cc_start: 0.5922 (t80) cc_final: 0.5660 (t80) REVERT: C 381 MET cc_start: 0.8236 (ptt) cc_final: 0.7758 (ppp) REVERT: E 224 GLN cc_start: 0.9210 (mt0) cc_final: 0.8909 (mm110) REVERT: E 303 TYR cc_start: 0.8742 (m-80) cc_final: 0.8433 (m-80) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.4126 time to fit residues: 202.5314 Evaluate side-chains 219 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN B 79 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN E 452 GLN ** F 564 ASN ** 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 = 0.4125 r_free = 0.4125 target = 0.083568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.059591 restraints weight = 360333.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.061410 restraints weight = 155162.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.062685 restraints weight = 98619.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.063425 restraints weight = 77254.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.063644 restraints weight = 68511.613| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 22213 Z= 0.325 Angle : 0.759 8.218 29945 Z= 0.430 Chirality : 0.044 0.167 3359 Planarity : 0.005 0.044 3858 Dihedral : 7.186 154.573 2975 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.63 % Favored : 98.34 % Rotamer: Outliers : 0.71 % Allowed : 4.55 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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: 0.86 (0.15), residues: 2707 helix: 0.79 (0.13), residues: 1340 sheet: 0.50 (0.25), residues: 409 loop : 0.55 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 386 TYR 0.019 0.002 TYR A 434 PHE 0.022 0.002 PHE F 606 TRP 0.016 0.002 TRP B 162 HIS 0.008 0.001 HIS C 240 Details of bonding type rmsd covalent geometry : bond 0.00632 (22213) covalent geometry : angle 0.75854 (29945) hydrogen bonds : bond 0.06297 ( 1248) hydrogen bonds : angle 5.81106 ( 3483) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 230 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ASN cc_start: 0.9095 (m-40) cc_final: 0.8884 (m110) REVERT: B 575 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8899 (mtp) REVERT: C 381 MET cc_start: 0.8156 (ptt) cc_final: 0.7827 (ppp) REVERT: C 383 ASP cc_start: 0.6779 (p0) cc_final: 0.6486 (p0) REVERT: D 44 PHE cc_start: 0.7022 (m-80) cc_final: 0.6672 (m-10) REVERT: D 152 ASP cc_start: 0.8201 (p0) cc_final: 0.7948 (p0) REVERT: D 346 VAL cc_start: 0.9472 (t) cc_final: 0.9255 (p) REVERT: E 259 MET cc_start: 0.6120 (mtp) cc_final: 0.5741 (mtp) REVERT: F 639 MET cc_start: -0.0080 (tpt) cc_final: -0.1171 (tpt) outliers start: 17 outliers final: 13 residues processed: 242 average time/residue: 0.3970 time to fit residues: 142.5511 Evaluate side-chains 206 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 LYS Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain F residue 745 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 245 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 360 ASN B 383 ASN B 415 ASN D 279 GLN E 452 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.084000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.060536 restraints weight = 366260.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.062382 restraints weight = 154603.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 75)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.063751 restraints weight = 96713.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.064194 restraints weight = 74992.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.064478 restraints weight = 68073.719| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22213 Z= 0.184 Angle : 0.602 6.871 29945 Z= 0.334 Chirality : 0.041 0.166 3359 Planarity : 0.004 0.057 3858 Dihedral : 6.734 157.513 2975 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.96 % Favored : 98.01 % Rotamer: Outliers : 0.63 % Allowed : 5.85 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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: 1.02 (0.16), residues: 2707 helix: 1.15 (0.13), residues: 1330 sheet: 0.24 (0.25), residues: 403 loop : 0.42 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 400 TYR 0.015 0.002 TYR E 468 PHE 0.021 0.002 PHE F 606 TRP 0.015 0.002 TRP B 162 HIS 0.006 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00365 (22213) covalent geometry : angle 0.60244 (29945) hydrogen bonds : bond 0.05161 ( 1248) hydrogen bonds : angle 5.35150 ( 3483) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 211 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 575 MET cc_start: 0.9110 (mtp) cc_final: 0.8819 (mtp) REVERT: C 381 MET cc_start: 0.8231 (ptt) cc_final: 0.7908 (ppp) REVERT: C 383 ASP cc_start: 0.6787 (p0) cc_final: 0.6457 (p0) REVERT: D 44 PHE cc_start: 0.7170 (m-80) cc_final: 0.6656 (m-10) REVERT: D 152 ASP cc_start: 0.8202 (p0) cc_final: 0.7933 (p0) REVERT: D 346 VAL cc_start: 0.9453 (t) cc_final: 0.9225 (p) outliers start: 15 outliers final: 13 residues processed: 217 average time/residue: 0.4042 time to fit residues: 130.6879 Evaluate side-chains 204 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 443 LYS Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain F residue 646 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 65 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 227 optimal weight: 7.9990 chunk 252 optimal weight: 20.0000 chunk 260 optimal weight: 30.0000 chunk 98 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 173 optimal weight: 0.0980 chunk 184 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN C 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.083843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.060387 restraints weight = 367334.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.062141 restraints weight = 158575.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.063495 restraints weight = 102019.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.064229 restraints weight = 79838.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.064420 restraints weight = 70818.647| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22213 Z= 0.168 Angle : 0.559 9.509 29945 Z= 0.305 Chirality : 0.041 0.139 3359 Planarity : 0.004 0.073 3858 Dihedral : 6.452 149.433 2975 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.48 % Favored : 97.49 % Rotamer: Outliers : 0.59 % Allowed : 6.94 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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: 0.94 (0.16), residues: 2707 helix: 1.19 (0.14), residues: 1341 sheet: -0.01 (0.25), residues: 405 loop : 0.29 (0.21), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 87 TYR 0.013 0.001 TYR E 468 PHE 0.017 0.001 PHE F 606 TRP 0.015 0.002 TRP F 600 HIS 0.007 0.001 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00340 (22213) covalent geometry : angle 0.55935 (29945) hydrogen bonds : bond 0.04601 ( 1248) hydrogen bonds : angle 5.16807 ( 3483) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 397 ASN cc_start: 0.8086 (t0) cc_final: 0.7853 (p0) REVERT: C 381 MET cc_start: 0.8226 (ptt) cc_final: 0.7962 (ppp) REVERT: C 383 ASP cc_start: 0.6583 (p0) cc_final: 0.6259 (p0) REVERT: D 44 PHE cc_start: 0.7096 (m-80) cc_final: 0.6638 (m-10) REVERT: D 152 ASP cc_start: 0.8146 (p0) cc_final: 0.7888 (p0) REVERT: D 346 VAL cc_start: 0.9428 (t) cc_final: 0.9219 (p) REVERT: E 499 MET cc_start: 0.9243 (tpp) cc_final: 0.8490 (tpp) outliers start: 14 outliers final: 10 residues processed: 206 average time/residue: 0.3937 time to fit residues: 122.0054 Evaluate side-chains 189 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 179 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 268 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 64 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 259 optimal weight: 30.0000 chunk 158 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN ** E 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 564 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.080988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.057578 restraints weight = 375250.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.059224 restraints weight = 165897.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.060432 restraints weight = 107761.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.060836 restraints weight = 85933.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.061372 restraints weight = 78467.566| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 22213 Z= 0.293 Angle : 0.648 6.592 29945 Z= 0.360 Chirality : 0.042 0.170 3359 Planarity : 0.005 0.060 3858 Dihedral : 6.682 155.360 2975 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.80 % Favored : 96.16 % Rotamer: Outliers : 1.13 % Allowed : 7.27 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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: 0.19 (0.16), residues: 2707 helix: 0.63 (0.13), residues: 1345 sheet: -0.44 (0.25), residues: 408 loop : -0.11 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 400 TYR 0.018 0.002 TYR E 468 PHE 0.026 0.002 PHE A 349 TRP 0.014 0.002 TRP B 162 HIS 0.006 0.002 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00589 (22213) covalent geometry : angle 0.64836 (29945) hydrogen bonds : bond 0.04783 ( 1248) hydrogen bonds : angle 5.50814 ( 3483) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 381 MET cc_start: 0.8275 (ptt) cc_final: 0.8023 (ppp) REVERT: C 383 ASP cc_start: 0.6420 (p0) cc_final: 0.5754 (t0) REVERT: D 44 PHE cc_start: 0.7561 (m-80) cc_final: 0.7062 (m-10) REVERT: D 152 ASP cc_start: 0.8153 (p0) cc_final: 0.7905 (p0) REVERT: E 499 MET cc_start: 0.9282 (tpp) cc_final: 0.8632 (tpp) REVERT: F 691 MET cc_start: 0.2891 (mmp) cc_final: 0.2651 (mmp) outliers start: 27 outliers final: 22 residues processed: 190 average time/residue: 0.3612 time to fit residues: 105.0557 Evaluate side-chains 185 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 443 LYS Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain F residue 745 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 18 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 169 optimal weight: 40.0000 chunk 160 optimal weight: 9.9990 chunk 125 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 261 optimal weight: 30.0000 chunk 247 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 234 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 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 = 0.4078 r_free = 0.4078 target = 0.081706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.058204 restraints weight = 373088.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.059882 restraints weight = 163006.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.061186 restraints weight = 105865.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.061875 restraints weight = 83963.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.062050 restraints weight = 75057.005| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22213 Z= 0.211 Angle : 0.573 6.332 29945 Z= 0.313 Chirality : 0.041 0.144 3359 Planarity : 0.004 0.055 3858 Dihedral : 6.604 158.039 2975 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 0.88 % Allowed : 8.32 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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 (0.16), residues: 2707 helix: 0.80 (0.13), residues: 1345 sheet: -0.59 (0.25), residues: 405 loop : -0.25 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 87 TYR 0.016 0.002 TYR E 468 PHE 0.013 0.001 PHE C 354 TRP 0.014 0.002 TRP B 162 HIS 0.006 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00423 (22213) covalent geometry : angle 0.57255 (29945) hydrogen bonds : bond 0.04398 ( 1248) hydrogen bonds : angle 5.28226 ( 3483) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 668 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8099 (tt0) REVERT: C 381 MET cc_start: 0.8290 (ptt) cc_final: 0.8028 (ppp) REVERT: C 383 ASP cc_start: 0.6456 (p0) cc_final: 0.5770 (t0) REVERT: D 44 PHE cc_start: 0.7442 (m-80) cc_final: 0.7002 (m-10) REVERT: D 152 ASP cc_start: 0.8178 (p0) cc_final: 0.7940 (p0) REVERT: D 268 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8667 (tm-30) REVERT: E 499 MET cc_start: 0.9275 (tpp) cc_final: 0.8615 (tpp) REVERT: F 691 MET cc_start: 0.2589 (mmp) cc_final: 0.2352 (mmp) outliers start: 21 outliers final: 14 residues processed: 183 average time/residue: 0.3823 time to fit residues: 107.6084 Evaluate side-chains 178 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain F residue 745 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 194 optimal weight: 0.6980 chunk 204 optimal weight: 6.9990 chunk 268 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 216 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 166 optimal weight: 50.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.081679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.058193 restraints weight = 371057.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.059838 restraints weight = 162584.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.061141 restraints weight = 105842.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.061552 restraints weight = 83908.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.062149 restraints weight = 76682.219| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22213 Z= 0.186 Angle : 0.555 6.339 29945 Z= 0.301 Chirality : 0.040 0.136 3359 Planarity : 0.004 0.054 3858 Dihedral : 6.505 156.013 2975 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 0.84 % Allowed : 8.15 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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: 0.33 (0.16), residues: 2707 helix: 0.95 (0.14), residues: 1338 sheet: -0.68 (0.25), residues: 404 loop : -0.23 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 87 TYR 0.016 0.001 TYR E 468 PHE 0.016 0.001 PHE D 198 TRP 0.014 0.002 TRP B 162 HIS 0.005 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00376 (22213) covalent geometry : angle 0.55466 (29945) hydrogen bonds : bond 0.04286 ( 1248) hydrogen bonds : angle 5.18364 ( 3483) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 668 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7947 (tt0) REVERT: C 381 MET cc_start: 0.8387 (ptt) cc_final: 0.8099 (ppp) REVERT: C 383 ASP cc_start: 0.6381 (p0) cc_final: 0.5758 (t0) REVERT: D 44 PHE cc_start: 0.7505 (m-80) cc_final: 0.7085 (m-10) REVERT: D 152 ASP cc_start: 0.8137 (p0) cc_final: 0.7893 (p0) REVERT: D 268 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8686 (tm-30) REVERT: E 499 MET cc_start: 0.9258 (tpp) cc_final: 0.8605 (tpp) REVERT: F 691 MET cc_start: 0.2590 (mmp) cc_final: 0.2353 (mmp) outliers start: 20 outliers final: 18 residues processed: 182 average time/residue: 0.3821 time to fit residues: 106.4865 Evaluate side-chains 183 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain F residue 745 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 107 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 112 optimal weight: 0.0870 chunk 20 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 257 optimal weight: 50.0000 chunk 31 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN B 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.082403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.058988 restraints weight = 372890.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.060632 restraints weight = 164387.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.061815 restraints weight = 104679.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.062204 restraints weight = 83510.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.062824 restraints weight = 76621.773| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22213 Z= 0.127 Angle : 0.524 6.678 29945 Z= 0.279 Chirality : 0.040 0.140 3359 Planarity : 0.004 0.055 3858 Dihedral : 6.324 154.306 2975 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.92 % Favored : 97.04 % Rotamer: Outliers : 0.63 % Allowed : 8.36 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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: 0.67 (0.16), residues: 2707 helix: 1.30 (0.14), residues: 1332 sheet: -0.66 (0.25), residues: 404 loop : -0.11 (0.21), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 87 TYR 0.013 0.001 TYR E 468 PHE 0.013 0.001 PHE C 354 TRP 0.015 0.001 TRP B 162 HIS 0.004 0.001 HIS E 247 Details of bonding type rmsd covalent geometry : bond 0.00259 (22213) covalent geometry : angle 0.52416 (29945) hydrogen bonds : bond 0.04028 ( 1248) hydrogen bonds : angle 4.92318 ( 3483) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 383 ASP cc_start: 0.6053 (p0) cc_final: 0.5437 (t0) REVERT: D 44 PHE cc_start: 0.7334 (m-80) cc_final: 0.6953 (m-10) REVERT: D 152 ASP cc_start: 0.8258 (p0) cc_final: 0.8016 (p0) REVERT: E 499 MET cc_start: 0.9252 (tpp) cc_final: 0.8612 (tpp) REVERT: F 691 MET cc_start: 0.2622 (mmp) cc_final: 0.2374 (mmp) outliers start: 15 outliers final: 12 residues processed: 181 average time/residue: 0.3811 time to fit residues: 104.5274 Evaluate side-chains 175 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain F residue 745 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 212 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 229 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN B 123 GLN E 292 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.081868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.058299 restraints weight = 373053.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.059951 restraints weight = 163224.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.061240 restraints weight = 106159.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.061922 restraints weight = 84505.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.062103 restraints weight = 75720.440| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22213 Z= 0.178 Angle : 0.548 8.253 29945 Z= 0.295 Chirality : 0.040 0.134 3359 Planarity : 0.004 0.055 3858 Dihedral : 6.306 152.971 2975 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 0.63 % Allowed : 8.57 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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: 0.59 (0.16), residues: 2707 helix: 1.24 (0.14), residues: 1331 sheet: -0.69 (0.25), residues: 406 loop : -0.15 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 87 TYR 0.014 0.001 TYR E 468 PHE 0.019 0.001 PHE F 606 TRP 0.014 0.002 TRP B 162 HIS 0.004 0.001 HIS E 247 Details of bonding type rmsd covalent geometry : bond 0.00359 (22213) covalent geometry : angle 0.54811 (29945) hydrogen bonds : bond 0.04049 ( 1248) hydrogen bonds : angle 5.00856 ( 3483) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 575 MET cc_start: 0.9048 (mtp) cc_final: 0.8824 (mpp) REVERT: C 383 ASP cc_start: 0.5724 (p0) cc_final: 0.5074 (t0) REVERT: D 44 PHE cc_start: 0.7503 (m-80) cc_final: 0.7122 (m-10) REVERT: D 152 ASP cc_start: 0.8249 (p0) cc_final: 0.8007 (p0) REVERT: E 499 MET cc_start: 0.9270 (tpp) cc_final: 0.8650 (tpp) REVERT: F 691 MET cc_start: 0.2453 (mmp) cc_final: 0.2200 (mmp) outliers start: 15 outliers final: 14 residues processed: 174 average time/residue: 0.3794 time to fit residues: 100.0342 Evaluate side-chains 172 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 291 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 231 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 252 optimal weight: 40.0000 chunk 191 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 258 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 411 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.081097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.057502 restraints weight = 380141.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.059082 restraints weight = 166376.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.059844 restraints weight = 109039.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.060886 restraints weight = 91517.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.061097 restraints weight = 80125.695| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22213 Z= 0.233 Angle : 0.596 7.999 29945 Z= 0.323 Chirality : 0.041 0.215 3359 Planarity : 0.004 0.050 3858 Dihedral : 6.399 151.052 2975 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.58 % Favored : 95.38 % Rotamer: Outliers : 0.75 % Allowed : 8.69 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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: 0.33 (0.16), residues: 2707 helix: 1.03 (0.14), residues: 1325 sheet: -0.75 (0.25), residues: 420 loop : -0.29 (0.21), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 87 TYR 0.015 0.002 TYR E 468 PHE 0.029 0.002 PHE F 606 TRP 0.013 0.002 TRP B 162 HIS 0.005 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00469 (22213) covalent geometry : angle 0.59603 (29945) hydrogen bonds : bond 0.04206 ( 1248) hydrogen bonds : angle 5.19884 ( 3483) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 383 ASP cc_start: 0.5475 (p0) cc_final: 0.4784 (t0) REVERT: D 44 PHE cc_start: 0.7696 (m-80) cc_final: 0.7331 (m-10) REVERT: D 152 ASP cc_start: 0.8208 (p0) cc_final: 0.7985 (p0) REVERT: E 499 MET cc_start: 0.9217 (tpp) cc_final: 0.8681 (tpp) REVERT: F 691 MET cc_start: 0.2450 (mmp) cc_final: 0.2208 (mmp) outliers start: 18 outliers final: 18 residues processed: 166 average time/residue: 0.3811 time to fit residues: 96.5896 Evaluate side-chains 169 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain F residue 745 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 235 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 132 optimal weight: 0.0870 chunk 127 optimal weight: 5.9990 chunk 264 optimal weight: 7.9990 chunk 49 optimal weight: 0.0980 chunk 169 optimal weight: 40.0000 chunk 124 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 160 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 overall best weight: 3.0364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 444 ASN B 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.081378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.058025 restraints weight = 377636.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.059573 restraints weight = 164740.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.060765 restraints weight = 106569.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.061439 restraints weight = 85511.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.061609 restraints weight = 76965.419| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22213 Z= 0.195 Angle : 0.566 8.004 29945 Z= 0.305 Chirality : 0.041 0.181 3359 Planarity : 0.004 0.052 3858 Dihedral : 6.364 147.833 2975 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.36 % Favored : 95.60 % Rotamer: Outliers : 0.67 % Allowed : 8.94 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.11 % 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: 0.35 (0.16), residues: 2707 helix: 1.10 (0.14), residues: 1325 sheet: -0.79 (0.25), residues: 403 loop : -0.36 (0.21), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 87 TYR 0.014 0.001 TYR E 468 PHE 0.022 0.001 PHE F 606 TRP 0.013 0.002 TRP B 162 HIS 0.005 0.001 HIS E 247 Details of bonding type rmsd covalent geometry : bond 0.00396 (22213) covalent geometry : angle 0.56580 (29945) hydrogen bonds : bond 0.04087 ( 1248) hydrogen bonds : angle 5.12378 ( 3483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9315.64 seconds wall clock time: 159 minutes 7.41 seconds (9547.41 seconds total)