Starting phenix.real_space_refine on Tue Jul 7 04:53:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kw7_23050/07_2026/7kw7_23050_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kw7_23050/07_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_23050/07_2026/7kw7_23050_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kw7_23050/07_2026/7kw7_23050_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kw7_23050/07_2026/7kw7_23050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kw7_23050/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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, 28 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Time building chain proxies: 7.26, per 1000 atoms: 0.17 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: 4.64 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: 1.01 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: 12.11 Time building geometry restraints manager: 6.22 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 3.470 ... (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: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.330 Extract box with map and model: 0.750 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 42.550 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: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 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/Z covalent geometry : bond 0.02107 / 1.12 (22213) covalent geometry : angle 1.73306 / 1.17 (29945) hydrogen bonds : bond 0.16314 / 10.82 ( 1248) hydrogen bonds : angle 6.96642 / 4.83 ( 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 : 1.142 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: 0.4011 time to fit residues: 199.6592 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 : 0.920 ------------------------------------------------------------------------------- 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... A 106 ASN B 79 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.083588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.059590 restraints weight = 361678.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.061412 restraints weight = 156635.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.062696 restraints weight = 99417.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.063142 restraints weight = 77745.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.063424 restraints weight = 70551.711| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 22213 Z= 0.317 Angle : 0.753 8.020 29945 Z= 0.423 Chirality : 0.044 0.175 3359 Planarity : 0.005 0.044 3858 Dihedral : 7.380 157.657 2975 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.74 % Favored : 98.23 % Rotamer: Outliers : 0.79 % Allowed : 4.47 % 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: 0.82 (0.15), residues: 2707 helix: 0.76 (0.13), residues: 1340 sheet: 0.49 (0.25), residues: 409 loop : 0.52 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 386 TYR 0.020 0.002 TYR A 434 PHE 0.020 0.002 PHE F 606 TRP 0.016 0.002 TRP B 162 HIS 0.007 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.32 (22213) covalent geometry : angle 0.75287 / 0.42 (29945) hydrogen bonds : bond 0.06196 / 4.07 ( 1248) hydrogen bonds : angle 5.84922 / 4.05 ( 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 253 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 234 time to evaluate : 1.191 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: A 415 ASN cc_start: 0.9090 (m-40) cc_final: 0.8880 (m110) REVERT: B 497 GLU cc_start: 0.8261 (tt0) cc_final: 0.7945 (tp30) REVERT: B 575 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8870 (mtp) REVERT: C 381 MET cc_start: 0.8156 (ptt) cc_final: 0.7827 (ppp) REVERT: C 383 ASP cc_start: 0.6769 (p0) cc_final: 0.6476 (p0) REVERT: D 44 PHE cc_start: 0.7030 (m-80) cc_final: 0.6763 (m-10) REVERT: D 152 ASP cc_start: 0.8190 (p0) cc_final: 0.7933 (p0) REVERT: E 259 MET cc_start: 0.6079 (mtp) cc_final: 0.5711 (mtp) REVERT: F 639 MET cc_start: 0.0543 (tpt) cc_final: -0.0604 (tpt) outliers start: 19 outliers final: 15 residues processed: 247 average time/residue: 0.3927 time to fit residues: 146.4202 Evaluate side-chains 212 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU 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 494 ILE 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: 9.9990 chunk 161 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 184 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 383 ASN B 415 ASN D 279 GLN E 452 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.083838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.060261 restraints weight = 366536.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.062169 restraints weight = 155276.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.063529 restraints weight = 97368.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.063985 restraints weight = 75670.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.064603 restraints weight = 68702.972| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22213 Z= 0.199 Angle : 0.611 7.062 29945 Z= 0.340 Chirality : 0.042 0.161 3359 Planarity : 0.004 0.046 3858 Dihedral : 6.849 163.534 2975 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.93 % Rotamer: Outliers : 0.71 % Allowed : 5.98 % Favored : 93.31 % 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: 0.90 (0.16), residues: 2707 helix: 1.02 (0.13), residues: 1332 sheet: 0.24 (0.25), residues: 405 loop : 0.37 (0.20), residues: 970 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 0.019 0.002 PHE F 606 TRP 0.016 0.002 TRP B 162 HIS 0.006 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.20 (22213) covalent geometry : angle 0.61083 / 0.34 (29945) hydrogen bonds : bond 0.05281 / 3.49 ( 1248) hydrogen bonds : angle 5.42720 / 3.76 ( 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 225 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 1.219 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: B 497 GLU cc_start: 0.8226 (tt0) cc_final: 0.7784 (tp30) REVERT: C 381 MET cc_start: 0.8224 (ptt) cc_final: 0.7888 (ppp) REVERT: C 383 ASP cc_start: 0.6798 (p0) cc_final: 0.6472 (p0) REVERT: D 44 PHE cc_start: 0.7293 (m-80) cc_final: 0.6787 (m-10) REVERT: D 152 ASP cc_start: 0.8178 (p0) cc_final: 0.7911 (p0) outliers start: 17 outliers final: 13 residues processed: 216 average time/residue: 0.4059 time to fit residues: 131.2215 Evaluate side-chains 201 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 227 optimal weight: 4.9990 chunk 252 optimal weight: 30.0000 chunk 260 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 173 optimal weight: 8.9990 chunk 184 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 ASN C 33 GLN ** E 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 564 ASN 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 = 0.081407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.058168 restraints weight = 380027.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.059858 restraints weight = 167939.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.060687 restraints weight = 107594.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.061623 restraints weight = 88710.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.061845 restraints weight = 77757.125| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 22213 Z= 0.289 Angle : 0.657 8.857 29945 Z= 0.365 Chirality : 0.042 0.153 3359 Planarity : 0.005 0.099 3858 Dihedral : 6.775 156.158 2975 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.32 % Favored : 96.64 % Rotamer: Outliers : 1.13 % Allowed : 6.48 % Favored : 92.39 % 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: 0.21 (0.16), residues: 2707 helix: 0.59 (0.13), residues: 1351 sheet: -0.23 (0.25), residues: 415 loop : -0.11 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 87 TYR 0.018 0.002 TYR E 468 PHE 0.018 0.002 PHE F 606 TRP 0.012 0.002 TRP B 162 HIS 0.007 0.002 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.29 (22213) covalent geometry : angle 0.65743 / 0.37 (29945) hydrogen bonds : bond 0.04961 / 3.26 ( 1248) hydrogen bonds : angle 5.59673 / 3.87 ( 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 213 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 1.199 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: B 397 ASN cc_start: 0.8151 (t0) cc_final: 0.7935 (p0) REVERT: B 497 GLU cc_start: 0.8271 (tt0) cc_final: 0.7833 (tp30) REVERT: C 381 MET cc_start: 0.8264 (ptt) cc_final: 0.7974 (ppp) REVERT: C 383 ASP cc_start: 0.6598 (p0) cc_final: 0.6287 (p0) REVERT: D 44 PHE cc_start: 0.7456 (m-80) cc_final: 0.6950 (m-10) REVERT: D 152 ASP cc_start: 0.8135 (p0) cc_final: 0.7870 (p0) REVERT: E 259 MET cc_start: 0.7364 (ptm) cc_final: 0.7043 (ptm) REVERT: E 499 MET cc_start: 0.9286 (tpp) cc_final: 0.8552 (tpp) outliers start: 27 outliers final: 21 residues processed: 203 average time/residue: 0.3884 time to fit residues: 120.6395 Evaluate side-chains 192 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 375 GLU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 443 LYS Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain B residue 35 ASN 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 375 GLU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 64 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 259 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.083131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.059498 restraints weight = 372242.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.061314 restraints weight = 159437.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.062696 restraints weight = 101596.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.063122 restraints weight = 79727.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.063703 restraints weight = 72693.935| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22213 Z= 0.139 Angle : 0.545 6.272 29945 Z= 0.294 Chirality : 0.041 0.174 3359 Planarity : 0.004 0.059 3858 Dihedral : 6.537 160.316 2975 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.51 % Favored : 97.45 % Rotamer: Outliers : 0.50 % Allowed : 8.02 % Favored : 91.48 % 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: 0.70 (0.16), residues: 2707 helix: 1.15 (0.14), residues: 1334 sheet: -0.27 (0.25), residues: 410 loop : 0.02 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 400 TYR 0.015 0.001 TYR B 38 PHE 0.022 0.001 PHE A 349 TRP 0.014 0.002 TRP B 162 HIS 0.005 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (22213) covalent geometry : angle 0.54528 / 0.29 (29945) hydrogen bonds : bond 0.04405 / 2.91 ( 1248) hydrogen bonds : angle 5.12027 / 3.54 ( 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 199 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 1.105 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: C 381 MET cc_start: 0.8238 (ptt) cc_final: 0.7983 (ppp) REVERT: C 383 ASP cc_start: 0.6459 (p0) cc_final: 0.5811 (t0) REVERT: D 44 PHE cc_start: 0.7248 (m-80) cc_final: 0.6859 (m-10) REVERT: D 152 ASP cc_start: 0.8163 (p0) cc_final: 0.7887 (p0) REVERT: D 381 MET cc_start: 0.8684 (mmm) cc_final: 0.8468 (mmp) REVERT: E 499 MET cc_start: 0.9264 (tpp) cc_final: 0.8579 (tpp) REVERT: F 691 MET cc_start: 0.2494 (mmp) cc_final: 0.2206 (mmp) outliers start: 12 outliers final: 9 residues processed: 194 average time/residue: 0.3595 time to fit residues: 107.8118 Evaluate side-chains 181 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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 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 187 ARG Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 232 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 18 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 169 optimal weight: 40.0000 chunk 160 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 261 optimal weight: 20.0000 chunk 247 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.081889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.058579 restraints weight = 370181.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.060234 restraints weight = 162949.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.061438 restraints weight = 104577.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.061856 restraints weight = 83160.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.062099 restraints weight = 75967.937| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22213 Z= 0.208 Angle : 0.564 6.199 29945 Z= 0.309 Chirality : 0.041 0.145 3359 Planarity : 0.004 0.057 3858 Dihedral : 6.509 158.867 2975 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 0.75 % Allowed : 8.32 % Favored : 90.93 % 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: 0.46 (0.16), residues: 2707 helix: 0.99 (0.14), residues: 1343 sheet: -0.42 (0.25), residues: 413 loop : -0.16 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 87 TYR 0.015 0.002 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/Z covalent geometry : bond 0.00417 / 0.21 (22213) covalent geometry : angle 0.56417 / 0.31 (29945) hydrogen bonds : bond 0.04354 / 2.86 ( 1248) hydrogen bonds : angle 5.21705 / 3.61 ( 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 190 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 1.123 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: C 381 MET cc_start: 0.8280 (ptt) cc_final: 0.8052 (ppp) REVERT: C 383 ASP cc_start: 0.6451 (p0) cc_final: 0.5757 (t0) REVERT: D 44 PHE cc_start: 0.7405 (m-80) cc_final: 0.6996 (m-10) REVERT: D 152 ASP cc_start: 0.8186 (p0) cc_final: 0.7928 (p0) REVERT: D 268 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8639 (tm-30) REVERT: E 499 MET cc_start: 0.9289 (tpp) cc_final: 0.8625 (tpp) REVERT: F 691 MET cc_start: 0.2715 (mmp) cc_final: 0.2474 (mmp) outliers start: 18 outliers final: 11 residues processed: 182 average time/residue: 0.3763 time to fit residues: 106.7609 Evaluate side-chains 176 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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 417 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 194 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 268 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 240 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 216 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.081943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.058464 restraints weight = 375937.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.060137 restraints weight = 166923.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.061379 restraints weight = 110232.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.062219 restraints weight = 87367.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.062442 restraints weight = 76953.538| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22213 Z= 0.176 Angle : 0.542 6.241 29945 Z= 0.294 Chirality : 0.040 0.141 3359 Planarity : 0.004 0.054 3858 Dihedral : 6.435 158.872 2975 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.71 % Rotamer: Outliers : 0.63 % Allowed : 8.23 % Favored : 91.14 % 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: 0.54 (0.16), residues: 2707 helix: 1.13 (0.14), residues: 1337 sheet: -0.52 (0.25), residues: 413 loop : -0.17 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 87 TYR 0.015 0.001 TYR E 468 PHE 0.012 0.001 PHE E 371 TRP 0.014 0.002 TRP B 162 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.18 (22213) covalent geometry : angle 0.54194 / 0.29 (29945) hydrogen bonds : bond 0.04205 / 2.76 ( 1248) hydrogen bonds : angle 5.09040 / 3.52 ( 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 185 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 1.090 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: A 668 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8075 (tt0) REVERT: B 98 MET cc_start: 0.8400 (tpp) cc_final: 0.8184 (tpp) REVERT: B 474 MET cc_start: 0.8201 (mtp) cc_final: 0.7897 (ttm) REVERT: C 383 ASP cc_start: 0.6378 (p0) cc_final: 0.5712 (t0) REVERT: D 44 PHE cc_start: 0.7470 (m-80) cc_final: 0.7062 (m-10) REVERT: D 152 ASP cc_start: 0.8261 (p0) cc_final: 0.8006 (p0) REVERT: E 499 MET cc_start: 0.9287 (tpp) cc_final: 0.8635 (tpp) REVERT: F 691 MET cc_start: 0.2664 (mmp) cc_final: 0.2416 (mmp) outliers start: 15 outliers final: 10 residues processed: 179 average time/residue: 0.3531 time to fit residues: 99.2205 Evaluate side-chains 174 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 417 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 107 optimal weight: 0.0070 chunk 167 optimal weight: 40.0000 chunk 70 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 257 optimal weight: 50.0000 chunk 31 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4089 r_free = 0.4089 target = 0.082533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.058811 restraints weight = 374148.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.060501 restraints weight = 163494.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.062018 restraints weight = 108230.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.062462 restraints weight = 83914.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.062736 restraints weight = 76230.683| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22213 Z= 0.127 Angle : 0.523 6.649 29945 Z= 0.278 Chirality : 0.040 0.166 3359 Planarity : 0.004 0.054 3858 Dihedral : 6.305 157.992 2975 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.81 % Favored : 97.16 % Rotamer: Outliers : 0.50 % Allowed : 8.61 % Favored : 90.89 % 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: 0.79 (0.16), residues: 2707 helix: 1.38 (0.14), residues: 1330 sheet: -0.48 (0.25), residues: 415 loop : -0.06 (0.21), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 400 TYR 0.012 0.001 TYR E 468 PHE 0.015 0.001 PHE D 198 TRP 0.014 0.001 TRP B 162 HIS 0.004 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (22213) covalent geometry : angle 0.52292 / 0.28 (29945) hydrogen bonds : bond 0.03995 / 2.63 ( 1248) hydrogen bonds : angle 4.90327 / 3.39 ( 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 191 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 1.237 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: B 98 MET cc_start: 0.8405 (tpp) cc_final: 0.8182 (tpp) REVERT: C 383 ASP cc_start: 0.6082 (p0) cc_final: 0.5424 (t0) REVERT: D 44 PHE cc_start: 0.7323 (m-80) cc_final: 0.6965 (m-10) REVERT: D 152 ASP cc_start: 0.8276 (p0) cc_final: 0.8036 (p0) REVERT: E 499 MET cc_start: 0.9266 (tpp) cc_final: 0.8613 (tpp) REVERT: F 691 MET cc_start: 0.2726 (mmp) cc_final: 0.2492 (mmp) outliers start: 12 outliers final: 10 residues processed: 186 average time/residue: 0.3668 time to fit residues: 105.4342 Evaluate side-chains 177 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 263 LEU Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain D residue 232 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 212 optimal weight: 4.9990 chunk 203 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 229 optimal weight: 0.8980 chunk 170 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4092 r_free = 0.4092 target = 0.082563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.059138 restraints weight = 372095.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.060794 restraints weight = 162377.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.062107 restraints weight = 104914.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.062476 restraints weight = 83317.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.062980 restraints weight = 76518.884| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22213 Z= 0.128 Angle : 0.520 7.143 29945 Z= 0.276 Chirality : 0.040 0.139 3359 Planarity : 0.004 0.051 3858 Dihedral : 6.237 157.546 2975 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.77 % Favored : 97.19 % Rotamer: Outliers : 0.42 % Allowed : 8.73 % Favored : 90.85 % 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: 0.87 (0.16), residues: 2707 helix: 1.48 (0.14), residues: 1329 sheet: -0.50 (0.25), residues: 421 loop : -0.04 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 400 TYR 0.016 0.001 TYR B 381 PHE 0.018 0.001 PHE F 606 TRP 0.014 0.001 TRP B 162 HIS 0.004 0.001 HIS E 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (22213) covalent geometry : angle 0.52041 / 0.28 (29945) hydrogen bonds : bond 0.03907 / 2.56 ( 1248) hydrogen bonds : angle 4.84379 / 3.35 ( 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 181 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 1.258 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: B 98 MET cc_start: 0.8394 (tpp) cc_final: 0.8176 (tpp) REVERT: C 383 ASP cc_start: 0.5839 (p0) cc_final: 0.5186 (t0) REVERT: D 44 PHE cc_start: 0.7314 (m-80) cc_final: 0.6971 (m-10) REVERT: D 152 ASP cc_start: 0.8284 (p0) cc_final: 0.8046 (p0) REVERT: E 499 MET cc_start: 0.9259 (tpp) cc_final: 0.8618 (tpp) REVERT: F 691 MET cc_start: 0.2606 (mmp) cc_final: 0.2358 (mmp) outliers start: 10 outliers final: 10 residues processed: 177 average time/residue: 0.3928 time to fit residues: 106.3696 Evaluate side-chains 173 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 263 LEU Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain D residue 232 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 231 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 252 optimal weight: 40.0000 chunk 191 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 258 optimal weight: 40.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.081206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.057626 restraints weight = 381244.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.059230 restraints weight = 165560.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.060469 restraints weight = 107778.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.060821 restraints weight = 86659.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.061334 restraints weight = 79806.274| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22213 Z= 0.225 Angle : 0.583 8.166 29945 Z= 0.316 Chirality : 0.041 0.222 3359 Planarity : 0.004 0.099 3858 Dihedral : 6.386 157.260 2975 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 0.46 % Allowed : 8.98 % 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: 0.50 (0.16), residues: 2707 helix: 1.17 (0.14), residues: 1329 sheet: -0.65 (0.25), residues: 420 loop : -0.24 (0.21), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 612 TYR 0.014 0.002 TYR E 468 PHE 0.028 0.002 PHE F 606 TRP 0.013 0.002 TRP B 162 HIS 0.005 0.001 HIS E 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.23 (22213) covalent geometry : angle 0.58294 / 0.32 (29945) hydrogen bonds : bond 0.04155 / 2.71 ( 1248) hydrogen bonds : angle 5.10549 / 3.53 ( 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 164 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 1.253 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: B 98 MET cc_start: 0.8478 (tpp) cc_final: 0.8266 (tpp) REVERT: B 497 GLU cc_start: 0.8296 (tt0) cc_final: 0.7970 (tp30) REVERT: C 383 ASP cc_start: 0.5686 (p0) cc_final: 0.4966 (t0) REVERT: D 44 PHE cc_start: 0.7678 (m-80) cc_final: 0.7318 (m-10) REVERT: D 152 ASP cc_start: 0.8221 (p0) cc_final: 0.7994 (p0) REVERT: D 218 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7824 (tm-30) REVERT: E 499 MET cc_start: 0.9235 (tpp) cc_final: 0.8680 (tpp) REVERT: F 691 MET cc_start: 0.2481 (mmp) cc_final: 0.2225 (mmp) outliers start: 11 outliers final: 11 residues processed: 160 average time/residue: 0.3896 time to fit residues: 97.0040 Evaluate side-chains 161 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 132 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 chunk 264 optimal weight: 50.0000 chunk 49 optimal weight: 0.7980 chunk 169 optimal weight: 30.0000 chunk 124 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4076 r_free = 0.4076 target = 0.081809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.058536 restraints weight = 378175.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.060070 restraints weight = 165598.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.061211 restraints weight = 106197.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.061622 restraints weight = 85609.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.062172 restraints weight = 78853.056| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22213 Z= 0.168 Angle : 0.543 7.167 29945 Z= 0.291 Chirality : 0.040 0.141 3359 Planarity : 0.004 0.049 3858 Dihedral : 6.325 156.310 2975 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.38 % Rotamer: Outliers : 0.50 % Allowed : 9.19 % Favored : 90.31 % 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: 1.29 (0.14), residues: 1329 sheet: -0.68 (0.25), residues: 418 loop : -0.22 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 612 TYR 0.013 0.001 TYR B 381 PHE 0.022 0.001 PHE F 606 TRP 0.014 0.001 TRP B 162 HIS 0.004 0.001 HIS E 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (22213) covalent geometry : angle 0.54338 / 0.29 (29945) hydrogen bonds : bond 0.03981 / 2.60 ( 1248) hydrogen bonds : angle 4.98759 / 3.45 ( 3483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8564.36 seconds wall clock time: 146 minutes 34.03 seconds (8794.03 seconds total)