Starting phenix.real_space_refine on Fri Mar 6 01:18:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oku_20105/03_2026/6oku_20105.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oku_20105/03_2026/6oku_20105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6oku_20105/03_2026/6oku_20105.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oku_20105/03_2026/6oku_20105.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oku_20105/03_2026/6oku_20105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oku_20105/03_2026/6oku_20105.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 16926 2.51 5 N 4368 2.21 5 O 5712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27048 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3864 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 472} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 3.43, per 1000 atoms: 0.13 Number of scatterers: 27048 At special positions: 0 Unit cell: (182.7, 179.8, 134.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 5712 8.00 N 4368 7.00 C 16926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 1.2 seconds 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6468 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 64 sheets defined 13.8% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 226 through 232 Processing helix chain 'A' and resid 272 through 278 removed outlier: 3.689A pdb=" N SER A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 506 through 513 removed outlier: 3.854A pdb=" N ILE A 510 " --> pdb=" O TYR A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 555 removed outlier: 3.659A pdb=" N PHE A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 593 removed outlier: 3.600A pdb=" N LYS A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 removed outlier: 3.603A pdb=" N VAL A 603 " --> pdb=" O ILE A 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 Processing helix chain 'B' and resid 272 through 278 removed outlier: 3.688A pdb=" N SER B 278 " --> pdb=" O TYR B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 506 through 513 removed outlier: 3.853A pdb=" N ILE B 510 " --> pdb=" O TYR B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 555 removed outlier: 3.660A pdb=" N PHE B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 593 removed outlier: 3.601A pdb=" N LYS B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 removed outlier: 3.602A pdb=" N VAL B 603 " --> pdb=" O ILE B 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 232 Processing helix chain 'C' and resid 272 through 278 removed outlier: 3.688A pdb=" N SER C 278 " --> pdb=" O TYR C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 506 through 513 removed outlier: 3.854A pdb=" N ILE C 510 " --> pdb=" O TYR C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 555 removed outlier: 3.659A pdb=" N PHE C 555 " --> pdb=" O ILE C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 593 removed outlier: 3.601A pdb=" N LYS C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 removed outlier: 3.603A pdb=" N VAL C 603 " --> pdb=" O ILE C 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 232 Processing helix chain 'D' and resid 272 through 278 removed outlier: 3.688A pdb=" N SER D 278 " --> pdb=" O TYR D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 503 through 505 No H-bonds generated for 'chain 'D' and resid 503 through 505' Processing helix chain 'D' and resid 506 through 513 removed outlier: 3.853A pdb=" N ILE D 510 " --> pdb=" O TYR D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 555 removed outlier: 3.659A pdb=" N PHE D 555 " --> pdb=" O ILE D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 593 removed outlier: 3.601A pdb=" N LYS D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 603 removed outlier: 3.602A pdb=" N VAL D 603 " --> pdb=" O ILE D 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 232 Processing helix chain 'E' and resid 272 through 278 removed outlier: 3.688A pdb=" N SER E 278 " --> pdb=" O TYR E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 463 through 472 Processing helix chain 'E' and resid 503 through 505 No H-bonds generated for 'chain 'E' and resid 503 through 505' Processing helix chain 'E' and resid 506 through 513 removed outlier: 3.854A pdb=" N ILE E 510 " --> pdb=" O TYR E 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 555 removed outlier: 3.660A pdb=" N PHE E 555 " --> pdb=" O ILE E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 593 removed outlier: 3.601A pdb=" N LYS E 593 " --> pdb=" O LYS E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 603 removed outlier: 3.603A pdb=" N VAL E 603 " --> pdb=" O ILE E 600 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 232 Processing helix chain 'F' and resid 272 through 278 removed outlier: 3.688A pdb=" N SER F 278 " --> pdb=" O TYR F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 503 through 505 No H-bonds generated for 'chain 'F' and resid 503 through 505' Processing helix chain 'F' and resid 506 through 513 removed outlier: 3.854A pdb=" N ILE F 510 " --> pdb=" O TYR F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 555 removed outlier: 3.659A pdb=" N PHE F 555 " --> pdb=" O ILE F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 593 removed outlier: 3.601A pdb=" N LYS F 593 " --> pdb=" O LYS F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 603 removed outlier: 3.603A pdb=" N VAL F 603 " --> pdb=" O ILE F 600 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 232 Processing helix chain 'G' and resid 272 through 278 removed outlier: 3.687A pdb=" N SER G 278 " --> pdb=" O TYR G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 290 Processing helix chain 'G' and resid 463 through 472 Processing helix chain 'G' and resid 503 through 505 No H-bonds generated for 'chain 'G' and resid 503 through 505' Processing helix chain 'G' and resid 506 through 513 removed outlier: 3.854A pdb=" N ILE G 510 " --> pdb=" O TYR G 506 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 555 removed outlier: 3.659A pdb=" N PHE G 555 " --> pdb=" O ILE G 551 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 593 removed outlier: 3.600A pdb=" N LYS G 593 " --> pdb=" O LYS G 589 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 removed outlier: 3.603A pdb=" N VAL G 603 " --> pdb=" O ILE G 600 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 299 through 311 removed outlier: 5.378A pdb=" N VAL A 300 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR A 398 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL A 302 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR A 396 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET A 304 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG A 394 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A 306 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 311 removed outlier: 5.378A pdb=" N VAL A 300 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR A 398 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL A 302 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR A 396 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET A 304 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG A 394 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A 306 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 314 through 326 removed outlier: 3.729A pdb=" N ASN A 371 " --> pdb=" O ARG B 325 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN B 371 " --> pdb=" O ARG C 325 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN C 371 " --> pdb=" O ARG D 325 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN D 371 " --> pdb=" O ARG E 325 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN E 371 " --> pdb=" O ARG F 325 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN F 371 " --> pdb=" O ARG G 325 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN G 371 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.611A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL A 406 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER A 484 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN A 482 " --> pdb=" O PRO A 408 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 490 removed outlier: 3.536A pdb=" N THR A 489 " --> pdb=" O VAL A 497 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 525 through 531 Processing sheet with id=AA8, first strand: chain 'A' and resid 558 through 560 removed outlier: 3.741A pdb=" N LEU A 564 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 618 through 619 removed outlier: 3.549A pdb=" N TYR A 618 " --> pdb=" O ILE A 738 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 651 through 659 removed outlier: 4.179A pdb=" N THR A 680 " --> pdb=" O SER A 728 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 695 " --> pdb=" O SER A 683 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AB3, first strand: chain 'B' and resid 299 through 311 removed outlier: 5.378A pdb=" N VAL B 300 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR B 398 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL B 302 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR B 396 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET B 304 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG B 394 " --> pdb=" O MET B 304 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 306 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 299 through 311 removed outlier: 5.378A pdb=" N VAL B 300 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR B 398 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL B 302 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR B 396 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET B 304 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG B 394 " --> pdb=" O MET B 304 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 306 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 418 through 423 removed outlier: 6.610A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LYS B 423 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL B 406 " --> pdb=" O SER B 484 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER B 484 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN B 482 " --> pdb=" O PRO B 408 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 489 through 490 removed outlier: 3.536A pdb=" N THR B 489 " --> pdb=" O VAL B 497 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 525 through 531 Processing sheet with id=AB8, first strand: chain 'B' and resid 558 through 560 removed outlier: 3.741A pdb=" N LEU B 564 " --> pdb=" O ILE B 571 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 618 through 619 removed outlier: 3.549A pdb=" N TYR B 618 " --> pdb=" O ILE B 738 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 651 through 659 removed outlier: 4.179A pdb=" N THR B 680 " --> pdb=" O SER B 728 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 695 " --> pdb=" O SER B 683 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AC3, first strand: chain 'C' and resid 299 through 311 removed outlier: 5.378A pdb=" N VAL C 300 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR C 398 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL C 302 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR C 396 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET C 304 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG C 394 " --> pdb=" O MET C 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS C 306 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 299 through 311 removed outlier: 5.378A pdb=" N VAL C 300 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR C 398 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL C 302 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR C 396 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET C 304 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG C 394 " --> pdb=" O MET C 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS C 306 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.611A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LYS C 423 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL C 406 " --> pdb=" O SER C 484 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER C 484 " --> pdb=" O VAL C 406 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN C 482 " --> pdb=" O PRO C 408 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 489 through 490 removed outlier: 3.536A pdb=" N THR C 489 " --> pdb=" O VAL C 497 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 525 through 531 Processing sheet with id=AC8, first strand: chain 'C' and resid 558 through 560 removed outlier: 3.741A pdb=" N LEU C 564 " --> pdb=" O ILE C 571 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 618 through 619 removed outlier: 3.549A pdb=" N TYR C 618 " --> pdb=" O ILE C 738 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 651 through 659 removed outlier: 4.179A pdb=" N THR C 680 " --> pdb=" O SER C 728 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR C 695 " --> pdb=" O SER C 683 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 235 through 238 Processing sheet with id=AD3, first strand: chain 'D' and resid 299 through 311 removed outlier: 5.378A pdb=" N VAL D 300 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR D 398 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL D 302 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR D 396 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET D 304 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG D 394 " --> pdb=" O MET D 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS D 306 " --> pdb=" O ASN D 392 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 299 through 311 removed outlier: 5.378A pdb=" N VAL D 300 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR D 398 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL D 302 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR D 396 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET D 304 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG D 394 " --> pdb=" O MET D 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS D 306 " --> pdb=" O ASN D 392 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.611A pdb=" N LEU D 412 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR D 421 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR D 410 " --> pdb=" O THR D 421 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LYS D 423 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL D 406 " --> pdb=" O SER D 484 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER D 484 " --> pdb=" O VAL D 406 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN D 482 " --> pdb=" O PRO D 408 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 489 through 490 removed outlier: 3.536A pdb=" N THR D 489 " --> pdb=" O VAL D 497 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 525 through 531 Processing sheet with id=AD8, first strand: chain 'D' and resid 558 through 560 removed outlier: 3.741A pdb=" N LEU D 564 " --> pdb=" O ILE D 571 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 618 through 619 removed outlier: 3.548A pdb=" N TYR D 618 " --> pdb=" O ILE D 738 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 651 through 659 removed outlier: 4.178A pdb=" N THR D 680 " --> pdb=" O SER D 728 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR D 695 " --> pdb=" O SER D 683 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AE3, first strand: chain 'E' and resid 299 through 311 removed outlier: 5.377A pdb=" N VAL E 300 " --> pdb=" O THR E 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR E 398 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL E 302 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR E 396 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET E 304 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG E 394 " --> pdb=" O MET E 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS E 306 " --> pdb=" O ASN E 392 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 299 through 311 removed outlier: 5.377A pdb=" N VAL E 300 " --> pdb=" O THR E 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR E 398 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL E 302 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR E 396 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET E 304 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG E 394 " --> pdb=" O MET E 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS E 306 " --> pdb=" O ASN E 392 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 418 through 423 removed outlier: 6.611A pdb=" N LEU E 412 " --> pdb=" O LEU E 419 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR E 421 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR E 410 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LYS E 423 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL E 406 " --> pdb=" O SER E 484 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER E 484 " --> pdb=" O VAL E 406 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN E 482 " --> pdb=" O PRO E 408 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 489 through 490 removed outlier: 3.535A pdb=" N THR E 489 " --> pdb=" O VAL E 497 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 525 through 531 Processing sheet with id=AE8, first strand: chain 'E' and resid 558 through 560 removed outlier: 3.741A pdb=" N LEU E 564 " --> pdb=" O ILE E 571 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 618 through 619 removed outlier: 3.549A pdb=" N TYR E 618 " --> pdb=" O ILE E 738 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 651 through 659 removed outlier: 4.179A pdb=" N THR E 680 " --> pdb=" O SER E 728 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR E 695 " --> pdb=" O SER E 683 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AF3, first strand: chain 'F' and resid 299 through 311 removed outlier: 5.378A pdb=" N VAL F 300 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR F 398 " --> pdb=" O VAL F 300 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL F 302 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N TYR F 396 " --> pdb=" O VAL F 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET F 304 " --> pdb=" O ARG F 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG F 394 " --> pdb=" O MET F 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS F 306 " --> pdb=" O ASN F 392 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 299 through 311 removed outlier: 5.378A pdb=" N VAL F 300 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR F 398 " --> pdb=" O VAL F 300 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL F 302 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N TYR F 396 " --> pdb=" O VAL F 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET F 304 " --> pdb=" O ARG F 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG F 394 " --> pdb=" O MET F 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS F 306 " --> pdb=" O ASN F 392 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 418 through 423 removed outlier: 6.611A pdb=" N LEU F 412 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR F 421 " --> pdb=" O THR F 410 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR F 410 " --> pdb=" O THR F 421 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LYS F 423 " --> pdb=" O PRO F 408 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL F 406 " --> pdb=" O SER F 484 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER F 484 " --> pdb=" O VAL F 406 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN F 482 " --> pdb=" O PRO F 408 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 489 through 490 removed outlier: 3.536A pdb=" N THR F 489 " --> pdb=" O VAL F 497 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 525 through 531 Processing sheet with id=AF8, first strand: chain 'F' and resid 558 through 560 removed outlier: 3.741A pdb=" N LEU F 564 " --> pdb=" O ILE F 571 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 618 through 619 removed outlier: 3.549A pdb=" N TYR F 618 " --> pdb=" O ILE F 738 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 651 through 659 removed outlier: 4.179A pdb=" N THR F 680 " --> pdb=" O SER F 728 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR F 695 " --> pdb=" O SER F 683 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 235 through 238 Processing sheet with id=AG3, first strand: chain 'G' and resid 299 through 311 removed outlier: 5.377A pdb=" N VAL G 300 " --> pdb=" O THR G 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR G 398 " --> pdb=" O VAL G 300 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL G 302 " --> pdb=" O TYR G 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR G 396 " --> pdb=" O VAL G 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET G 304 " --> pdb=" O ARG G 394 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG G 394 " --> pdb=" O MET G 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS G 306 " --> pdb=" O ASN G 392 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 299 through 311 removed outlier: 5.377A pdb=" N VAL G 300 " --> pdb=" O THR G 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR G 398 " --> pdb=" O VAL G 300 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL G 302 " --> pdb=" O TYR G 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR G 396 " --> pdb=" O VAL G 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET G 304 " --> pdb=" O ARG G 394 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG G 394 " --> pdb=" O MET G 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS G 306 " --> pdb=" O ASN G 392 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.611A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LYS G 423 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL G 406 " --> pdb=" O SER G 484 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER G 484 " --> pdb=" O VAL G 406 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN G 482 " --> pdb=" O PRO G 408 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 489 through 490 removed outlier: 3.535A pdb=" N THR G 489 " --> pdb=" O VAL G 497 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 525 through 531 Processing sheet with id=AG8, first strand: chain 'G' and resid 558 through 560 removed outlier: 3.741A pdb=" N LEU G 564 " --> pdb=" O ILE G 571 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 618 through 619 removed outlier: 3.549A pdb=" N TYR G 618 " --> pdb=" O ILE G 738 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 651 through 659 removed outlier: 4.179A pdb=" N THR G 680 " --> pdb=" O SER G 728 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR G 695 " --> pdb=" O SER G 683 " (cutoff:3.500A) 875 hydrogen bonds defined for protein. 2352 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: 5.44 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8774 1.34 - 1.45: 4193 1.45 - 1.57: 14473 1.57 - 1.69: 0 1.69 - 1.80: 77 Bond restraints: 27517 Sorted by residual: bond pdb=" C LYS A 541 " pdb=" N THR A 542 " ideal model delta sigma weight residual 1.331 1.295 0.035 1.24e-02 6.50e+03 8.16e+00 bond pdb=" C LYS B 541 " pdb=" N THR B 542 " ideal model delta sigma weight residual 1.331 1.295 0.035 1.24e-02 6.50e+03 8.13e+00 bond pdb=" C LYS D 541 " pdb=" N THR D 542 " ideal model delta sigma weight residual 1.331 1.295 0.035 1.24e-02 6.50e+03 8.08e+00 bond pdb=" C LYS F 541 " pdb=" N THR F 542 " ideal model delta sigma weight residual 1.331 1.296 0.035 1.24e-02 6.50e+03 7.92e+00 bond pdb=" C LYS G 541 " pdb=" N THR G 542 " ideal model delta sigma weight residual 1.331 1.296 0.034 1.24e-02 6.50e+03 7.64e+00 ... (remaining 27512 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 36996 3.65 - 7.31: 272 7.31 - 10.96: 42 10.96 - 14.62: 0 14.62 - 18.27: 7 Bond angle restraints: 37317 Sorted by residual: angle pdb=" CA LEU B 698 " pdb=" CB LEU B 698 " pdb=" CG LEU B 698 " ideal model delta sigma weight residual 116.30 134.57 -18.27 3.50e+00 8.16e-02 2.72e+01 angle pdb=" CA LEU D 698 " pdb=" CB LEU D 698 " pdb=" CG LEU D 698 " ideal model delta sigma weight residual 116.30 134.56 -18.26 3.50e+00 8.16e-02 2.72e+01 angle pdb=" CA LEU A 698 " pdb=" CB LEU A 698 " pdb=" CG LEU A 698 " ideal model delta sigma weight residual 116.30 134.56 -18.26 3.50e+00 8.16e-02 2.72e+01 angle pdb=" CA LEU E 698 " pdb=" CB LEU E 698 " pdb=" CG LEU E 698 " ideal model delta sigma weight residual 116.30 134.54 -18.24 3.50e+00 8.16e-02 2.72e+01 angle pdb=" CA LEU C 698 " pdb=" CB LEU C 698 " pdb=" CG LEU C 698 " ideal model delta sigma weight residual 116.30 134.53 -18.23 3.50e+00 8.16e-02 2.71e+01 ... (remaining 37312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 14609 16.99 - 33.98: 1624 33.98 - 50.97: 413 50.97 - 67.96: 84 67.96 - 84.95: 35 Dihedral angle restraints: 16765 sinusoidal: 6664 harmonic: 10101 Sorted by residual: dihedral pdb=" CA TYR F 732 " pdb=" C TYR F 732 " pdb=" N LEU F 733 " pdb=" CA LEU F 733 " ideal model delta harmonic sigma weight residual 180.00 152.19 27.81 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA TYR D 732 " pdb=" C TYR D 732 " pdb=" N LEU D 733 " pdb=" CA LEU D 733 " ideal model delta harmonic sigma weight residual 180.00 152.20 27.80 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA TYR C 732 " pdb=" C TYR C 732 " pdb=" N LEU C 733 " pdb=" CA LEU C 733 " ideal model delta harmonic sigma weight residual 180.00 152.20 27.80 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 16762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2549 0.045 - 0.090: 1178 0.090 - 0.135: 389 0.135 - 0.181: 85 0.181 - 0.226: 20 Chirality restraints: 4221 Sorted by residual: chirality pdb=" CB ILE E 547 " pdb=" CA ILE E 547 " pdb=" CG1 ILE E 547 " pdb=" CG2 ILE E 547 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE F 547 " pdb=" CA ILE F 547 " pdb=" CG1 ILE F 547 " pdb=" CG2 ILE F 547 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE D 547 " pdb=" CA ILE D 547 " pdb=" CG1 ILE D 547 " pdb=" CG2 ILE D 547 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 4218 not shown) Planarity restraints: 4858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 510 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.58e+00 pdb=" C ILE E 510 " -0.048 2.00e-02 2.50e+03 pdb=" O ILE E 510 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP E 511 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 510 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C ILE D 510 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE D 510 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP D 511 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 510 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C ILE F 510 " -0.047 2.00e-02 2.50e+03 pdb=" O ILE F 510 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP F 511 " 0.016 2.00e-02 2.50e+03 ... (remaining 4855 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3144 2.74 - 3.28: 25374 3.28 - 3.82: 43397 3.82 - 4.36: 46765 4.36 - 4.90: 84221 Nonbonded interactions: 202901 Sorted by model distance: nonbonded pdb=" OG1 THR A 638 " pdb=" OD1 ASN A 648 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR E 638 " pdb=" OD1 ASN E 648 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR C 638 " pdb=" OD1 ASN C 648 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR F 638 " pdb=" OD1 ASN F 648 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR D 638 " pdb=" OD1 ASN D 648 " model vdw 2.203 3.040 ... (remaining 202896 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.280 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 27517 Z= 0.336 Angle : 1.008 18.269 37317 Z= 0.555 Chirality : 0.057 0.226 4221 Planarity : 0.006 0.060 4858 Dihedral : 15.775 84.946 10297 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.69 % Favored : 88.31 % Rotamer: Outliers : 2.97 % Allowed : 8.68 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.09 (0.12), residues: 3423 helix: -3.76 (0.13), residues: 448 sheet: -1.00 (0.16), residues: 1008 loop : -3.58 (0.11), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 458 TYR 0.019 0.002 TYR B 261 PHE 0.032 0.004 PHE A 281 TRP 0.009 0.002 TRP B 375 HIS 0.008 0.005 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00742 (27517) covalent geometry : angle 1.00843 (37317) hydrogen bonds : bond 0.15917 ( 840) hydrogen bonds : angle 7.64444 ( 2352) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 232 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7186 (m-10) cc_final: 0.6170 (m-10) REVERT: A 379 LEU cc_start: 0.8511 (tt) cc_final: 0.8127 (mp) REVERT: A 400 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8745 (p) REVERT: A 707 PHE cc_start: 0.8155 (p90) cc_final: 0.7479 (p90) REVERT: A 741 LEU cc_start: 0.7717 (tp) cc_final: 0.7348 (tp) REVERT: B 417 ASP cc_start: 0.7471 (p0) cc_final: 0.7132 (p0) REVERT: B 707 PHE cc_start: 0.7876 (p90) cc_final: 0.7632 (p90) REVERT: C 313 GLU cc_start: 0.6366 (mm-30) cc_final: 0.6131 (mm-30) REVERT: D 707 PHE cc_start: 0.8276 (p90) cc_final: 0.7712 (p90) REVERT: E 313 GLU cc_start: 0.7271 (mm-30) cc_final: 0.7010 (mm-30) REVERT: E 314 HIS cc_start: 0.7160 (m-70) cc_final: 0.6897 (m90) REVERT: E 379 LEU cc_start: 0.8330 (tt) cc_final: 0.7879 (mp) REVERT: E 400 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.8666 (p) REVERT: E 403 MET cc_start: 0.8450 (tpt) cc_final: 0.8220 (tpp) REVERT: E 417 ASP cc_start: 0.7554 (p0) cc_final: 0.7269 (p0) REVERT: E 707 PHE cc_start: 0.8163 (p90) cc_final: 0.7963 (p90) REVERT: F 379 LEU cc_start: 0.8246 (tt) cc_final: 0.7983 (mp) REVERT: F 537 ASP cc_start: 0.8398 (t70) cc_final: 0.8010 (t0) REVERT: F 707 PHE cc_start: 0.8268 (p90) cc_final: 0.7947 (p90) REVERT: G 230 TYR cc_start: 0.6789 (m-10) cc_final: 0.5898 (m-80) REVERT: G 495 GLN cc_start: 0.7851 (pm20) cc_final: 0.7643 (pm20) REVERT: G 707 PHE cc_start: 0.8246 (p90) cc_final: 0.7927 (p90) outliers start: 91 outliers final: 37 residues processed: 302 average time/residue: 0.1794 time to fit residues: 86.4247 Evaluate side-chains 192 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 718 SER Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 688 ILE Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 688 ILE Chi-restraints excluded: chain E residue 718 SER Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 688 ILE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 409 THR Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 688 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN C 252 GLN C 390 ASN D 252 GLN D 431 ASN D 432 ASN E 252 GLN E 431 ASN F 252 GLN F 390 ASN G 252 GLN G 390 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.107319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.081153 restraints weight = 70363.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.081370 restraints weight = 50003.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.081544 restraints weight = 37051.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.081792 restraints weight = 33934.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.081973 restraints weight = 32766.629| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 27517 Z= 0.181 Angle : 0.648 12.058 37317 Z= 0.344 Chirality : 0.045 0.172 4221 Planarity : 0.004 0.046 4858 Dihedral : 6.977 57.561 3748 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.87 % Allowed : 12.49 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.12), residues: 3423 helix: -2.69 (0.18), residues: 462 sheet: -0.84 (0.16), residues: 973 loop : -3.20 (0.12), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 232 TYR 0.013 0.001 TYR A 666 PHE 0.020 0.002 PHE B 281 TRP 0.022 0.001 TRP C 375 HIS 0.004 0.001 HIS E 314 Details of bonding type rmsd covalent geometry : bond 0.00409 (27517) covalent geometry : angle 0.64824 (37317) hydrogen bonds : bond 0.04030 ( 840) hydrogen bonds : angle 6.03718 ( 2352) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 170 time to evaluate : 0.948 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: A 281 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.6812 (p90) REVERT: A 400 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8563 (p) REVERT: A 660 MET cc_start: 0.7678 (mmm) cc_final: 0.7260 (ttt) REVERT: A 707 PHE cc_start: 0.8223 (p90) cc_final: 0.7642 (p90) REVERT: A 741 LEU cc_start: 0.7484 (tp) cc_final: 0.7253 (tp) REVERT: B 232 ARG cc_start: 0.8263 (mmm-85) cc_final: 0.7967 (mmm-85) REVERT: B 281 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.7314 (p90) REVERT: B 660 MET cc_start: 0.7592 (mmm) cc_final: 0.7263 (ttt) REVERT: B 692 GLU cc_start: 0.5704 (OUTLIER) cc_final: 0.5393 (mp0) REVERT: B 707 PHE cc_start: 0.8114 (p90) cc_final: 0.7736 (p90) REVERT: B 743 SER cc_start: 0.4302 (OUTLIER) cc_final: 0.3659 (t) REVERT: C 538 PRO cc_start: 0.8988 (Cg_endo) cc_final: 0.8627 (Cg_exo) REVERT: C 743 SER cc_start: 0.4660 (OUTLIER) cc_final: 0.4043 (t) REVERT: D 707 PHE cc_start: 0.8170 (p90) cc_final: 0.7465 (p90) REVERT: E 281 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.6912 (p90) REVERT: E 707 PHE cc_start: 0.8158 (p90) cc_final: 0.7789 (p90) REVERT: F 281 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7152 (p90) REVERT: F 682 ASN cc_start: 0.7639 (p0) cc_final: 0.7433 (p0) REVERT: F 707 PHE cc_start: 0.8465 (p90) cc_final: 0.7890 (p90) REVERT: F 743 SER cc_start: 0.5140 (OUTLIER) cc_final: 0.4746 (t) REVERT: G 281 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7396 (p90) REVERT: G 660 MET cc_start: 0.7598 (mmm) cc_final: 0.7310 (ttt) REVERT: G 707 PHE cc_start: 0.8460 (p90) cc_final: 0.7901 (p90) outliers start: 88 outliers final: 58 residues processed: 253 average time/residue: 0.1666 time to fit residues: 68.0489 Evaluate side-chains 196 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 128 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 685 ILE Chi-restraints excluded: chain F residue 686 VAL Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain F residue 743 SER Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 409 THR Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 692 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 49 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN A 431 ASN A 432 ASN B 390 ASN B 431 ASN ** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 ASN D 390 ASN ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 ASN F 223 ASN F 431 ASN F 432 ASN G 431 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.102692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.076258 restraints weight = 72725.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.076973 restraints weight = 46421.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.077573 restraints weight = 35922.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.077835 restraints weight = 31907.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.077929 restraints weight = 29101.914| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 27517 Z= 0.321 Angle : 0.796 14.512 37317 Z= 0.416 Chirality : 0.049 0.168 4221 Planarity : 0.005 0.053 4858 Dihedral : 7.484 59.461 3720 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 5.22 % Allowed : 15.69 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.13), residues: 3423 helix: -2.61 (0.19), residues: 469 sheet: -0.78 (0.16), residues: 1022 loop : -3.14 (0.12), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 528 TYR 0.027 0.002 TYR C 230 PHE 0.030 0.003 PHE G 281 TRP 0.023 0.002 TRP D 375 HIS 0.003 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00740 (27517) covalent geometry : angle 0.79558 (37317) hydrogen bonds : bond 0.04791 ( 840) hydrogen bonds : angle 6.43799 ( 2352) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 112 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.6953 (p90) REVERT: A 660 MET cc_start: 0.7739 (mmm) cc_final: 0.6860 (ttt) REVERT: A 663 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8260 (pp) REVERT: A 713 THR cc_start: 0.5768 (m) cc_final: 0.5072 (p) REVERT: B 232 ARG cc_start: 0.8229 (mmm-85) cc_final: 0.7997 (mmm-85) REVERT: B 281 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7620 (p90) REVERT: B 644 GLN cc_start: 0.6369 (OUTLIER) cc_final: 0.6104 (pm20) REVERT: B 707 PHE cc_start: 0.8329 (p90) cc_final: 0.7791 (p90) REVERT: C 281 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7097 (p90) REVERT: C 538 PRO cc_start: 0.8977 (Cg_endo) cc_final: 0.8628 (Cg_exo) REVERT: D 281 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.6938 (p90) REVERT: E 281 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7371 (p90) REVERT: E 644 GLN cc_start: 0.5877 (OUTLIER) cc_final: 0.5675 (pm20) REVERT: E 663 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8531 (mt) REVERT: E 713 THR cc_start: 0.5332 (m) cc_final: 0.5130 (p) REVERT: F 223 ASN cc_start: 0.6668 (OUTLIER) cc_final: 0.5921 (p0) REVERT: F 230 TYR cc_start: 0.6855 (OUTLIER) cc_final: 0.5302 (m-80) REVERT: F 281 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7339 (p90) REVERT: F 707 PHE cc_start: 0.8430 (p90) cc_final: 0.7793 (p90) REVERT: G 281 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7431 (p90) REVERT: G 644 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.6503 (pm20) REVERT: G 660 MET cc_start: 0.7915 (mmm) cc_final: 0.7429 (ttt) REVERT: G 663 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8415 (mt) outliers start: 160 outliers final: 98 residues processed: 265 average time/residue: 0.1440 time to fit residues: 65.3030 Evaluate side-chains 213 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 100 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 537 ASP Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 644 GLN Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain E residue 695 THR Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 230 TYR Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 685 ILE Chi-restraints excluded: chain F residue 686 VAL Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 409 THR Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 462 ILE Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 644 GLN Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain G residue 686 VAL Chi-restraints excluded: chain G residue 692 GLU Chi-restraints excluded: chain G residue 695 THR Chi-restraints excluded: chain G residue 698 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 62 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 285 optimal weight: 20.0000 chunk 269 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 255 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 ASN B 682 ASN E 735 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.106322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.080010 restraints weight = 70945.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.080904 restraints weight = 42126.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.081234 restraints weight = 31876.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.081608 restraints weight = 28561.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.081706 restraints weight = 25743.242| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27517 Z= 0.145 Angle : 0.628 14.250 37317 Z= 0.324 Chirality : 0.044 0.152 4221 Planarity : 0.004 0.050 4858 Dihedral : 6.363 59.081 3713 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 4.21 % Allowed : 16.47 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.13), residues: 3423 helix: -1.85 (0.22), residues: 427 sheet: -0.44 (0.17), residues: 952 loop : -2.82 (0.12), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 668 TYR 0.015 0.001 TYR F 230 PHE 0.021 0.002 PHE B 281 TRP 0.026 0.002 TRP E 375 HIS 0.003 0.001 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.00327 (27517) covalent geometry : angle 0.62774 (37317) hydrogen bonds : bond 0.03566 ( 840) hydrogen bonds : angle 5.64083 ( 2352) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 126 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 PHE cc_start: 0.7020 (OUTLIER) cc_final: 0.6599 (p90) REVERT: A 643 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6944 (mt) REVERT: A 660 MET cc_start: 0.7529 (mmm) cc_final: 0.6747 (ttt) REVERT: A 713 THR cc_start: 0.5608 (m) cc_final: 0.5000 (p) REVERT: A 733 LEU cc_start: 0.5519 (OUTLIER) cc_final: 0.5309 (pp) REVERT: B 232 ARG cc_start: 0.8245 (mmm-85) cc_final: 0.8024 (mmm-85) REVERT: B 281 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.7361 (p90) REVERT: B 707 PHE cc_start: 0.8165 (p90) cc_final: 0.7716 (p90) REVERT: C 281 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.6754 (p90) REVERT: C 403 MET cc_start: 0.8184 (tpt) cc_final: 0.7611 (tpt) REVERT: C 538 PRO cc_start: 0.9106 (Cg_endo) cc_final: 0.8797 (Cg_exo) REVERT: D 281 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.7028 (p90) REVERT: D 537 ASP cc_start: 0.7908 (t70) cc_final: 0.7488 (t0) REVERT: D 664 LYS cc_start: 0.8980 (mmmt) cc_final: 0.8699 (tppt) REVERT: D 707 PHE cc_start: 0.8078 (p90) cc_final: 0.7568 (p90) REVERT: D 733 LEU cc_start: 0.5445 (OUTLIER) cc_final: 0.5090 (pp) REVERT: E 230 TYR cc_start: 0.7310 (OUTLIER) cc_final: 0.6934 (t80) REVERT: E 281 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.6830 (p90) REVERT: E 400 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8326 (t) REVERT: E 538 PRO cc_start: 0.9156 (Cg_endo) cc_final: 0.8900 (Cg_exo) REVERT: E 735 ASN cc_start: 0.8216 (m110) cc_final: 0.8004 (m-40) REVERT: F 281 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7307 (p90) REVERT: F 538 PRO cc_start: 0.9138 (Cg_endo) cc_final: 0.8932 (Cg_exo) REVERT: F 707 PHE cc_start: 0.8351 (p90) cc_final: 0.7741 (p90) REVERT: F 713 THR cc_start: 0.5385 (m) cc_final: 0.4999 (p) REVERT: F 733 LEU cc_start: 0.5352 (OUTLIER) cc_final: 0.5051 (pp) REVERT: G 281 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7462 (p90) REVERT: G 733 LEU cc_start: 0.4928 (OUTLIER) cc_final: 0.4553 (pp) outliers start: 129 outliers final: 78 residues processed: 244 average time/residue: 0.1523 time to fit residues: 63.8793 Evaluate side-chains 202 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 110 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain E residue 230 TYR Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 537 ASP Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain E residue 741 LEU Chi-restraints excluded: chain F residue 230 TYR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 692 GLU Chi-restraints excluded: chain G residue 733 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 195 optimal weight: 10.0000 chunk 241 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 339 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 178 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 223 ASN G 432 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.104192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.078688 restraints weight = 71583.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.078801 restraints weight = 45252.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.079120 restraints weight = 35446.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.079338 restraints weight = 33499.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.079473 restraints weight = 31224.874| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 27517 Z= 0.221 Angle : 0.688 14.811 37317 Z= 0.357 Chirality : 0.046 0.154 4221 Planarity : 0.004 0.049 4858 Dihedral : 6.539 59.822 3711 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 5.45 % Allowed : 16.31 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.13), residues: 3423 helix: -1.82 (0.22), residues: 427 sheet: -0.57 (0.16), residues: 1029 loop : -2.74 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 528 TYR 0.029 0.002 TYR C 230 PHE 0.026 0.003 PHE E 281 TRP 0.029 0.002 TRP E 375 HIS 0.004 0.002 HIS C 314 Details of bonding type rmsd covalent geometry : bond 0.00512 (27517) covalent geometry : angle 0.68796 (37317) hydrogen bonds : bond 0.03965 ( 840) hydrogen bonds : angle 5.82340 ( 2352) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 114 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 TYR cc_start: 0.6970 (OUTLIER) cc_final: 0.6056 (t80) REVERT: A 281 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.6939 (p90) REVERT: A 660 MET cc_start: 0.7510 (mmm) cc_final: 0.6813 (ttt) REVERT: A 663 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8349 (pp) REVERT: A 709 TYR cc_start: 0.6729 (m-80) cc_final: 0.6146 (m-10) REVERT: A 713 THR cc_start: 0.5626 (m) cc_final: 0.4931 (p) REVERT: B 643 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6927 (mp) REVERT: C 281 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.6979 (p90) REVERT: C 403 MET cc_start: 0.8115 (tpt) cc_final: 0.7600 (ttt) REVERT: C 538 PRO cc_start: 0.9135 (Cg_endo) cc_final: 0.8845 (Cg_exo) REVERT: C 660 MET cc_start: 0.6956 (ttt) cc_final: 0.5650 (tmm) REVERT: D 664 LYS cc_start: 0.9041 (mmmt) cc_final: 0.8753 (tppt) REVERT: D 707 PHE cc_start: 0.8106 (p90) cc_final: 0.7621 (p90) REVERT: E 223 ASN cc_start: 0.6303 (OUTLIER) cc_final: 0.5960 (p0) REVERT: E 281 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7230 (p90) REVERT: E 400 THR cc_start: 0.9190 (OUTLIER) cc_final: 0.8386 (t) REVERT: E 643 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6520 (mt) REVERT: E 663 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8808 (mt) REVERT: F 230 TYR cc_start: 0.6089 (OUTLIER) cc_final: 0.4252 (m-80) REVERT: F 281 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7243 (p90) REVERT: F 707 PHE cc_start: 0.8349 (p90) cc_final: 0.7828 (p90) REVERT: F 713 THR cc_start: 0.5385 (m) cc_final: 0.4923 (p) REVERT: F 733 LEU cc_start: 0.5550 (OUTLIER) cc_final: 0.5255 (pp) REVERT: G 230 TYR cc_start: 0.6102 (OUTLIER) cc_final: 0.5878 (m-80) REVERT: G 643 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6767 (mt) REVERT: G 663 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8551 (mt) outliers start: 167 outliers final: 121 residues processed: 269 average time/residue: 0.1457 time to fit residues: 67.9775 Evaluate side-chains 242 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 105 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 537 ASP Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain E residue 695 THR Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain E residue 741 LEU Chi-restraints excluded: chain F residue 230 TYR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 686 VAL Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain G residue 230 TYR Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 603 VAL Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 643 LEU Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain G residue 686 VAL Chi-restraints excluded: chain G residue 692 GLU Chi-restraints excluded: chain G residue 695 THR Chi-restraints excluded: chain G residue 698 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 164 optimal weight: 5.9990 chunk 246 optimal weight: 8.9990 chunk 207 optimal weight: 20.0000 chunk 280 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 chunk 138 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 297 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.105559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.079213 restraints weight = 71208.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.080330 restraints weight = 43388.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.080517 restraints weight = 31420.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.080789 restraints weight = 29853.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.080980 restraints weight = 27340.541| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 27517 Z= 0.161 Angle : 0.631 14.749 37317 Z= 0.326 Chirality : 0.044 0.169 4221 Planarity : 0.004 0.048 4858 Dihedral : 6.276 59.658 3711 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 5.28 % Allowed : 16.89 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.13), residues: 3423 helix: -1.60 (0.23), residues: 427 sheet: -0.15 (0.17), residues: 938 loop : -2.73 (0.12), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 528 TYR 0.027 0.001 TYR C 230 PHE 0.021 0.002 PHE E 281 TRP 0.031 0.002 TRP E 375 HIS 0.003 0.001 HIS C 314 Details of bonding type rmsd covalent geometry : bond 0.00367 (27517) covalent geometry : angle 0.63080 (37317) hydrogen bonds : bond 0.03533 ( 840) hydrogen bonds : angle 5.55257 ( 2352) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 121 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 TYR cc_start: 0.6712 (OUTLIER) cc_final: 0.6001 (t80) REVERT: A 281 PHE cc_start: 0.7089 (OUTLIER) cc_final: 0.6792 (p90) REVERT: A 660 MET cc_start: 0.7613 (mmm) cc_final: 0.6817 (ttt) REVERT: A 663 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8328 (pp) REVERT: A 709 TYR cc_start: 0.6697 (m-80) cc_final: 0.6111 (m-10) REVERT: A 713 THR cc_start: 0.5569 (m) cc_final: 0.4931 (p) REVERT: B 643 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6905 (mt) REVERT: B 707 PHE cc_start: 0.8337 (p90) cc_final: 0.7793 (p90) REVERT: C 281 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.6751 (p90) REVERT: C 403 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7782 (ttt) REVERT: C 538 PRO cc_start: 0.9106 (Cg_endo) cc_final: 0.8803 (Cg_exo) REVERT: C 660 MET cc_start: 0.6830 (ttt) cc_final: 0.5719 (tmm) REVERT: D 537 ASP cc_start: 0.7939 (t70) cc_final: 0.7562 (t0) REVERT: D 664 LYS cc_start: 0.9014 (mmmt) cc_final: 0.8721 (tppt) REVERT: D 707 PHE cc_start: 0.8016 (p90) cc_final: 0.7551 (p90) REVERT: E 281 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.7015 (p90) REVERT: E 400 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8374 (t) REVERT: E 538 PRO cc_start: 0.9141 (Cg_endo) cc_final: 0.8870 (Cg_exo) REVERT: E 643 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6428 (mt) REVERT: E 663 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8854 (mt) REVERT: F 230 TYR cc_start: 0.6735 (OUTLIER) cc_final: 0.4836 (m-80) REVERT: F 281 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7392 (p90) REVERT: F 707 PHE cc_start: 0.8288 (p90) cc_final: 0.7791 (p90) REVERT: F 713 THR cc_start: 0.5370 (m) cc_final: 0.4909 (p) REVERT: F 733 LEU cc_start: 0.5501 (OUTLIER) cc_final: 0.5271 (pp) REVERT: G 230 TYR cc_start: 0.6056 (OUTLIER) cc_final: 0.5781 (m-80) REVERT: G 281 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7469 (p90) REVERT: G 643 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6615 (mt) REVERT: G 663 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8538 (mt) outliers start: 162 outliers final: 120 residues processed: 265 average time/residue: 0.1498 time to fit residues: 69.2254 Evaluate side-chains 250 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 113 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 732 TYR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 537 ASP Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain E residue 695 THR Chi-restraints excluded: chain E residue 741 LEU Chi-restraints excluded: chain F residue 230 TYR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 603 VAL Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 686 VAL Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain G residue 230 TYR Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 603 VAL Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 643 LEU Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain G residue 692 GLU Chi-restraints excluded: chain G residue 695 THR Chi-restraints excluded: chain G residue 698 LEU Chi-restraints excluded: chain G residue 713 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 165 optimal weight: 0.0000 chunk 67 optimal weight: 0.5980 chunk 341 optimal weight: 20.0000 chunk 219 optimal weight: 5.9990 chunk 262 optimal weight: 4.9990 chunk 254 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 339 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 311 optimal weight: 7.9990 chunk 320 optimal weight: 6.9990 overall best weight: 2.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.105420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.078673 restraints weight = 71050.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.080329 restraints weight = 42358.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.080955 restraints weight = 29151.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.081273 restraints weight = 26773.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.081373 restraints weight = 24282.663| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 27517 Z= 0.167 Angle : 0.624 14.815 37317 Z= 0.323 Chirality : 0.044 0.169 4221 Planarity : 0.004 0.047 4858 Dihedral : 6.204 59.897 3711 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 5.51 % Allowed : 17.06 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.14), residues: 3423 helix: -1.50 (0.23), residues: 427 sheet: -0.33 (0.16), residues: 1015 loop : -2.64 (0.13), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 528 TYR 0.025 0.001 TYR E 230 PHE 0.022 0.002 PHE E 281 TRP 0.033 0.002 TRP E 375 HIS 0.003 0.002 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00383 (27517) covalent geometry : angle 0.62442 (37317) hydrogen bonds : bond 0.03527 ( 840) hydrogen bonds : angle 5.50295 ( 2352) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 121 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 TYR cc_start: 0.6821 (OUTLIER) cc_final: 0.6081 (t80) REVERT: A 281 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6824 (p90) REVERT: A 663 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8331 (pp) REVERT: A 709 TYR cc_start: 0.6677 (m-80) cc_final: 0.6126 (m-10) REVERT: A 713 THR cc_start: 0.5469 (m) cc_final: 0.5094 (p) REVERT: B 281 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.6927 (p90) REVERT: B 400 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8533 (t) REVERT: C 281 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.6797 (p90) REVERT: C 403 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7732 (ttt) REVERT: C 538 PRO cc_start: 0.9100 (Cg_endo) cc_final: 0.8785 (Cg_exo) REVERT: D 281 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7273 (p90) REVERT: D 664 LYS cc_start: 0.9090 (mmmt) cc_final: 0.8819 (tppt) REVERT: D 707 PHE cc_start: 0.7994 (p90) cc_final: 0.7528 (p90) REVERT: E 281 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.7110 (p90) REVERT: E 400 THR cc_start: 0.9207 (OUTLIER) cc_final: 0.8441 (t) REVERT: E 643 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6482 (mt) REVERT: E 663 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8825 (mt) REVERT: E 664 LYS cc_start: 0.9098 (mmmt) cc_final: 0.8895 (tppt) REVERT: F 230 TYR cc_start: 0.7034 (OUTLIER) cc_final: 0.4955 (m-80) REVERT: F 281 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7058 (p90) REVERT: F 707 PHE cc_start: 0.8262 (p90) cc_final: 0.7781 (p90) REVERT: F 713 THR cc_start: 0.5721 (m) cc_final: 0.5247 (p) REVERT: F 733 LEU cc_start: 0.5389 (OUTLIER) cc_final: 0.5083 (pp) REVERT: G 230 TYR cc_start: 0.6003 (OUTLIER) cc_final: 0.5722 (m-80) REVERT: G 281 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7383 (p90) REVERT: G 643 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6631 (mt) outliers start: 169 outliers final: 132 residues processed: 274 average time/residue: 0.1465 time to fit residues: 69.6536 Evaluate side-chains 264 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 114 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 732 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 422 ILE Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 537 ASP Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain E residue 695 THR Chi-restraints excluded: chain E residue 741 LEU Chi-restraints excluded: chain F residue 230 TYR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 603 VAL Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 685 ILE Chi-restraints excluded: chain F residue 686 VAL Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain G residue 230 TYR Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 603 VAL Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 643 LEU Chi-restraints excluded: chain G residue 686 VAL Chi-restraints excluded: chain G residue 692 GLU Chi-restraints excluded: chain G residue 695 THR Chi-restraints excluded: chain G residue 698 LEU Chi-restraints excluded: chain G residue 713 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 65 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 321 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 332 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.107470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.081483 restraints weight = 70862.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.081945 restraints weight = 45461.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.082183 restraints weight = 33234.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.082451 restraints weight = 31862.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.082609 restraints weight = 28690.227| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27517 Z= 0.117 Angle : 0.591 14.828 37317 Z= 0.301 Chirality : 0.043 0.198 4221 Planarity : 0.003 0.044 4858 Dihedral : 5.875 59.986 3711 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 4.63 % Allowed : 17.97 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.14), residues: 3423 helix: -1.25 (0.24), residues: 427 sheet: 0.06 (0.17), residues: 938 loop : -2.62 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 232 TYR 0.019 0.001 TYR C 230 PHE 0.016 0.002 PHE E 281 TRP 0.032 0.002 TRP E 375 HIS 0.002 0.001 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00263 (27517) covalent geometry : angle 0.59143 (37317) hydrogen bonds : bond 0.03098 ( 840) hydrogen bonds : angle 5.17604 ( 2352) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 134 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 TYR cc_start: 0.6644 (OUTLIER) cc_final: 0.6034 (t80) REVERT: A 403 MET cc_start: 0.8245 (tpt) cc_final: 0.7832 (tpt) REVERT: A 663 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8754 (pp) REVERT: A 707 PHE cc_start: 0.7934 (p90) cc_final: 0.7216 (p90) REVERT: A 713 THR cc_start: 0.5564 (m) cc_final: 0.5308 (p) REVERT: B 262 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8747 (tp) REVERT: B 281 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.6968 (p90) REVERT: B 400 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8488 (t) REVERT: B 707 PHE cc_start: 0.8237 (p90) cc_final: 0.7731 (p90) REVERT: C 281 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.6542 (p90) REVERT: C 403 MET cc_start: 0.8146 (tpt) cc_final: 0.7805 (ttt) REVERT: C 538 PRO cc_start: 0.9022 (Cg_endo) cc_final: 0.8740 (Cg_exo) REVERT: C 660 MET cc_start: 0.6823 (tmm) cc_final: 0.6544 (ttt) REVERT: D 281 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7179 (p90) REVERT: D 537 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7516 (t0) REVERT: D 707 PHE cc_start: 0.7947 (p90) cc_final: 0.7626 (p90) REVERT: E 400 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.8424 (t) REVERT: E 663 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8858 (mt) REVERT: E 664 LYS cc_start: 0.9070 (mmmt) cc_final: 0.8825 (tppt) REVERT: F 660 MET cc_start: 0.6204 (ttt) cc_final: 0.5498 (tmm) REVERT: F 707 PHE cc_start: 0.8228 (p90) cc_final: 0.7748 (p90) REVERT: F 713 THR cc_start: 0.5546 (m) cc_final: 0.5017 (p) REVERT: F 732 TYR cc_start: 0.4358 (OUTLIER) cc_final: 0.3160 (p90) REVERT: F 733 LEU cc_start: 0.5149 (OUTLIER) cc_final: 0.4933 (pp) REVERT: G 281 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7590 (p90) REVERT: G 643 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6594 (mt) REVERT: G 707 PHE cc_start: 0.8262 (p90) cc_final: 0.7824 (p90) outliers start: 142 outliers final: 113 residues processed: 261 average time/residue: 0.1449 time to fit residues: 65.8612 Evaluate side-chains 244 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 117 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 732 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain E residue 695 THR Chi-restraints excluded: chain E residue 741 LEU Chi-restraints excluded: chain F residue 230 TYR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 603 VAL Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain F residue 686 VAL Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 732 TYR Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 603 VAL Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 643 LEU Chi-restraints excluded: chain G residue 686 VAL Chi-restraints excluded: chain G residue 692 GLU Chi-restraints excluded: chain G residue 695 THR Chi-restraints excluded: chain G residue 713 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 15 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 332 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 243 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 735 ASN E 735 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.107751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.081091 restraints weight = 70854.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.082226 restraints weight = 43725.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.082883 restraints weight = 30344.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.083102 restraints weight = 27850.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.083339 restraints weight = 25604.062| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27517 Z= 0.117 Angle : 0.592 15.348 37317 Z= 0.300 Chirality : 0.044 0.191 4221 Planarity : 0.003 0.043 4858 Dihedral : 5.746 59.800 3711 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 4.79 % Allowed : 18.13 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.14), residues: 3423 helix: -1.10 (0.24), residues: 427 sheet: -0.06 (0.16), residues: 1015 loop : -2.55 (0.13), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 458 TYR 0.019 0.001 TYR C 230 PHE 0.016 0.002 PHE E 281 TRP 0.033 0.002 TRP D 375 HIS 0.003 0.001 HIS G 314 Details of bonding type rmsd covalent geometry : bond 0.00266 (27517) covalent geometry : angle 0.59248 (37317) hydrogen bonds : bond 0.03036 ( 840) hydrogen bonds : angle 5.00346 ( 2352) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 128 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 TYR cc_start: 0.6700 (OUTLIER) cc_final: 0.6019 (t80) REVERT: A 403 MET cc_start: 0.8275 (tpt) cc_final: 0.7982 (tpt) REVERT: A 663 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8650 (mt) REVERT: A 707 PHE cc_start: 0.7635 (p90) cc_final: 0.7429 (p90) REVERT: A 713 THR cc_start: 0.5663 (m) cc_final: 0.5316 (p) REVERT: B 262 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8754 (tp) REVERT: B 281 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.6935 (p90) REVERT: B 400 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8568 (t) REVERT: C 262 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8336 (tp) REVERT: C 281 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6553 (p90) REVERT: C 403 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7787 (ttt) REVERT: C 538 PRO cc_start: 0.9024 (Cg_endo) cc_final: 0.8720 (Cg_exo) REVERT: D 281 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7100 (p90) REVERT: D 537 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7495 (t0) REVERT: D 707 PHE cc_start: 0.7936 (p90) cc_final: 0.7505 (p90) REVERT: E 400 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8437 (t) REVERT: E 663 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8877 (mt) REVERT: E 664 LYS cc_start: 0.9063 (mmmt) cc_final: 0.8827 (tppt) REVERT: F 660 MET cc_start: 0.6020 (ttt) cc_final: 0.5393 (tmm) REVERT: F 707 PHE cc_start: 0.8230 (p90) cc_final: 0.7777 (p90) REVERT: F 710 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.6393 (mt-10) REVERT: F 713 THR cc_start: 0.5568 (m) cc_final: 0.5054 (p) REVERT: F 732 TYR cc_start: 0.4354 (OUTLIER) cc_final: 0.3185 (p90) REVERT: F 733 LEU cc_start: 0.4896 (OUTLIER) cc_final: 0.4656 (pp) REVERT: G 281 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7533 (p90) REVERT: G 643 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6625 (mt) REVERT: G 663 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8568 (mt) REVERT: G 707 PHE cc_start: 0.8253 (p90) cc_final: 0.7704 (p90) outliers start: 147 outliers final: 118 residues processed: 255 average time/residue: 0.1465 time to fit residues: 65.0559 Evaluate side-chains 258 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 122 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 732 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 732 TYR Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 422 ILE Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain E residue 695 THR Chi-restraints excluded: chain E residue 741 LEU Chi-restraints excluded: chain F residue 230 TYR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 603 VAL Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 686 VAL Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 710 GLU Chi-restraints excluded: chain F residue 732 TYR Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 462 ILE Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 603 VAL Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 643 LEU Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain G residue 686 VAL Chi-restraints excluded: chain G residue 692 GLU Chi-restraints excluded: chain G residue 695 THR Chi-restraints excluded: chain G residue 713 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 124 optimal weight: 7.9990 chunk 275 optimal weight: 0.3980 chunk 303 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 281 optimal weight: 0.6980 chunk 272 optimal weight: 2.9990 chunk 302 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 735 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.108256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.081986 restraints weight = 70991.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.082648 restraints weight = 44848.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.083019 restraints weight = 32806.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.083309 restraints weight = 30512.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.083537 restraints weight = 27557.327| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27517 Z= 0.110 Angle : 0.585 15.597 37317 Z= 0.294 Chirality : 0.043 0.188 4221 Planarity : 0.003 0.042 4858 Dihedral : 5.576 59.294 3711 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 4.40 % Allowed : 18.62 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.14), residues: 3423 helix: -0.99 (0.24), residues: 427 sheet: 0.00 (0.16), residues: 1015 loop : -2.51 (0.13), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 232 TYR 0.019 0.001 TYR C 666 PHE 0.015 0.002 PHE E 281 TRP 0.034 0.002 TRP E 375 HIS 0.002 0.001 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00249 (27517) covalent geometry : angle 0.58478 (37317) hydrogen bonds : bond 0.02917 ( 840) hydrogen bonds : angle 4.90652 ( 2352) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 130 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 TYR cc_start: 0.6633 (OUTLIER) cc_final: 0.5984 (t80) REVERT: A 403 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7989 (tpt) REVERT: A 663 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8718 (pp) REVERT: B 262 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8792 (tp) REVERT: B 281 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.6882 (p90) REVERT: B 400 THR cc_start: 0.9207 (OUTLIER) cc_final: 0.8571 (t) REVERT: C 262 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8336 (tp) REVERT: C 281 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.6412 (p90) REVERT: C 403 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7742 (ttt) REVERT: C 538 PRO cc_start: 0.9020 (Cg_endo) cc_final: 0.8723 (Cg_exo) REVERT: D 281 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.6996 (p90) REVERT: D 537 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7520 (t0) REVERT: D 707 PHE cc_start: 0.7934 (p90) cc_final: 0.7629 (p90) REVERT: E 400 THR cc_start: 0.9207 (OUTLIER) cc_final: 0.8419 (t) REVERT: E 664 LYS cc_start: 0.9067 (mmmt) cc_final: 0.8846 (tppt) REVERT: F 707 PHE cc_start: 0.8232 (p90) cc_final: 0.7791 (p90) REVERT: F 713 THR cc_start: 0.5503 (m) cc_final: 0.5062 (p) REVERT: F 732 TYR cc_start: 0.4197 (OUTLIER) cc_final: 0.3171 (p90) REVERT: F 733 LEU cc_start: 0.4756 (OUTLIER) cc_final: 0.4518 (pp) REVERT: G 281 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7446 (p90) REVERT: G 643 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6273 (mt) REVERT: G 663 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8565 (mt) REVERT: G 707 PHE cc_start: 0.8257 (p90) cc_final: 0.7756 (p90) outliers start: 135 outliers final: 111 residues processed: 246 average time/residue: 0.1413 time to fit residues: 60.5726 Evaluate side-chains 250 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 122 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 732 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 732 TYR Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain E residue 695 THR Chi-restraints excluded: chain E residue 732 TYR Chi-restraints excluded: chain E residue 741 LEU Chi-restraints excluded: chain F residue 230 TYR Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 603 VAL Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 686 VAL Chi-restraints excluded: chain F residue 732 TYR Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 462 ILE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 603 VAL Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 643 LEU Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain G residue 686 VAL Chi-restraints excluded: chain G residue 695 THR Chi-restraints excluded: chain G residue 713 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 276 optimal weight: 0.0370 chunk 191 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 238 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 236 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 5.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN E 735 ASN ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.103035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.077171 restraints weight = 71709.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.078031 restraints weight = 44675.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.078819 restraints weight = 33174.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.078954 restraints weight = 30690.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.079035 restraints weight = 27474.700| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 27517 Z= 0.285 Angle : 0.749 15.486 37317 Z= 0.389 Chirality : 0.048 0.273 4221 Planarity : 0.004 0.046 4858 Dihedral : 6.511 59.400 3709 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.10 % Favored : 88.90 % Rotamer: Outliers : 4.96 % Allowed : 18.17 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.14), residues: 3423 helix: -1.62 (0.23), residues: 434 sheet: -0.23 (0.16), residues: 987 loop : -2.65 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 528 TYR 0.033 0.002 TYR C 230 PHE 0.036 0.003 PHE A 281 TRP 0.041 0.003 TRP E 375 HIS 0.005 0.003 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00661 (27517) covalent geometry : angle 0.74930 (37317) hydrogen bonds : bond 0.04183 ( 840) hydrogen bonds : angle 5.81198 ( 2352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3588.56 seconds wall clock time: 63 minutes 50.22 seconds (3830.22 seconds total)