Starting phenix.real_space_refine on Thu Aug 6 04:34:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wmf_66089/08_2026/9wmf_66089.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wmf_66089/08_2026/9wmf_66089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wmf_66089/08_2026/9wmf_66089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wmf_66089/08_2026/9wmf_66089.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wmf_66089/08_2026/9wmf_66089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wmf_66089/08_2026/9wmf_66089.map" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 32 5.16 5 C 8406 2.51 5 N 2222 2.21 5 O 2392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13068 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6363 Classifications: {'peptide': 779} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 745} Chain: "C" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 171 Classifications: {'DNA': 8} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 7} Chain: "B" Number of atoms: 6363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6363 Classifications: {'peptide': 779} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 745} Chain: "D" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 171 Classifications: {'DNA': 8} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 7} Time building chain proxies: 3.11, per 1000 atoms: 0.24 Number of scatterers: 13068 At special positions: 0 Unit cell: (127.1, 127.1, 89.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 16 15.00 O 2392 8.00 N 2222 7.00 C 8406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 571.8 milliseconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2956 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 24 sheets defined 34.1% alpha, 21.8% beta 0 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 34 through 54 Processing helix chain 'A' and resid 105 through 126 removed outlier: 3.959A pdb=" N ASP A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL A 111 " --> pdb=" O HIS A 107 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 removed outlier: 4.139A pdb=" N TYR A 188 " --> pdb=" O CYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 199 through 202 removed outlier: 3.947A pdb=" N LYS A 202 " --> pdb=" O ASN A 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 199 through 202' Processing helix chain 'A' and resid 240 through 250 removed outlier: 4.286A pdb=" N HIS A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.503A pdb=" N SER A 298 " --> pdb=" O ARG A 295 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS A 300 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR A 301 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 302 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 370 through 383 removed outlier: 3.805A pdb=" N LYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE A 379 " --> pdb=" O ARG A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 423 Processing helix chain 'A' and resid 441 through 457 Processing helix chain 'A' and resid 474 through 490 removed outlier: 4.146A pdb=" N LYS A 486 " --> pdb=" O HIS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 527 through 546 Processing helix chain 'A' and resid 604 through 620 removed outlier: 4.202A pdb=" N LEU A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 656 Processing helix chain 'A' and resid 735 through 748 Processing helix chain 'A' and resid 761 through 771 removed outlier: 3.931A pdb=" N ILE A 767 " --> pdb=" O ILE A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 775 Processing helix chain 'B' and resid 34 through 54 Processing helix chain 'B' and resid 105 through 126 removed outlier: 4.001A pdb=" N ASP B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL B 111 " --> pdb=" O HIS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 188 Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 199 through 202 removed outlier: 4.107A pdb=" N LYS B 202 " --> pdb=" O ASN B 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 199 through 202' Processing helix chain 'B' and resid 240 through 250 removed outlier: 4.178A pdb=" N HIS B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 removed outlier: 4.139A pdb=" N ARG B 257 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 298 Processing helix chain 'B' and resid 299 through 304 removed outlier: 4.031A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE B 304 " --> pdb=" O HIS B 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 299 through 304' Processing helix chain 'B' and resid 306 through 322 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 370 through 383 removed outlier: 3.555A pdb=" N LYS B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE B 379 " --> pdb=" O ARG B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 423 Processing helix chain 'B' and resid 441 through 457 Processing helix chain 'B' and resid 474 through 489 removed outlier: 3.540A pdb=" N LEU B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 486 " --> pdb=" O HIS B 482 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 527 through 546 Processing helix chain 'B' and resid 604 through 620 removed outlier: 4.214A pdb=" N LEU B 608 " --> pdb=" O ARG B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 656 Processing helix chain 'B' and resid 735 through 748 Processing helix chain 'B' and resid 761 through 772 removed outlier: 4.104A pdb=" N ILE B 767 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU B 772 " --> pdb=" O ASP B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 775 No H-bonds generated for 'chain 'B' and resid 773 through 775' Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 10 removed outlier: 5.476A pdb=" N GLU A 155 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 62 removed outlier: 5.384A pdb=" N PHE A 66 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE A 26 " --> pdb=" O PHE A 66 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 68 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TYR A 21 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU A 95 " --> pdb=" O TYR A 21 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU A 23 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 79 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 278 through 281 removed outlier: 4.702A pdb=" N LYS A 224 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N SER A 267 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N PHE A 222 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N THR A 269 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU A 220 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 230 through 233 Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 327 Processing sheet with id=AA7, first strand: chain 'A' and resid 358 through 359 Processing sheet with id=AA8, first strand: chain 'A' and resid 430 through 434 Processing sheet with id=AA9, first strand: chain 'A' and resid 466 through 467 Processing sheet with id=AB1, first strand: chain 'A' and resid 507 through 510 Processing sheet with id=AB2, first strand: chain 'A' and resid 583 through 590 removed outlier: 4.658A pdb=" N GLN A 583 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 578 " --> pdb=" O GLN A 583 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE A 561 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL A 633 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 563 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP A 635 " --> pdb=" O ILE A 563 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE A 565 " --> pdb=" O ASP A 635 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE A 630 " --> pdb=" O GLY A 667 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL A 669 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE A 632 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU A 671 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ARG A 634 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N TYR A 666 " --> pdb=" O GLY A 732 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY A 732 " --> pdb=" O TYR A 666 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 668 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 726 " --> pdb=" O HIS A 672 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLU A 706 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER A 698 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AB4, first strand: chain 'B' and resid 8 through 10 Processing sheet with id=AB5, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.537A pdb=" N ALA B 69 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N PHE B 66 " --> pdb=" O PHE B 26 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N PHE B 26 " --> pdb=" O PHE B 66 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 68 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 70 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR B 21 " --> pdb=" O GLU B 95 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLU B 95 " --> pdb=" O TYR B 21 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU B 23 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 79 " --> pdb=" O ILE B 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 130 through 132 removed outlier: 5.311A pdb=" N GLU B 155 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 278 through 281 removed outlier: 4.602A pdb=" N SER B 265 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY B 221 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR B 269 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU B 219 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 230 through 233 Processing sheet with id=AB9, first strand: chain 'B' and resid 326 through 327 Processing sheet with id=AC1, first strand: chain 'B' and resid 358 through 359 removed outlier: 3.903A pdb=" N LEU B 351 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 430 through 434 Processing sheet with id=AC3, first strand: chain 'B' and resid 466 through 467 Processing sheet with id=AC4, first strand: chain 'B' and resid 507 through 511 removed outlier: 3.561A pdb=" N LYS B 508 " --> pdb=" O ARG B 522 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG B 522 " --> pdb=" O LYS B 508 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 583 through 586 removed outlier: 4.669A pdb=" N GLN B 583 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 578 " --> pdb=" O GLN B 583 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 583 through 586 removed outlier: 4.669A pdb=" N GLN B 583 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 578 " --> pdb=" O GLN B 583 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 565 " --> pdb=" O VAL B 633 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL B 567 " --> pdb=" O ASP B 635 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 630 " --> pdb=" O GLY B 667 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL B 669 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ILE B 632 " --> pdb=" O VAL B 669 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 671 " --> pdb=" O ILE B 632 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ARG B 634 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TYR B 666 " --> pdb=" O GLY B 732 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLY B 732 " --> pdb=" O TYR B 666 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL B 668 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 703 " --> pdb=" O GLU B 706 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE B 708 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU B 701 " --> pdb=" O PHE B 708 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE B 710 " --> pdb=" O TYR B 699 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR B 699 " --> pdb=" O PHE B 710 " (cutoff:3.500A) 527 hydrogen bonds defined for protein. 1473 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2096 1.32 - 1.44: 3736 1.44 - 1.57: 7494 1.57 - 1.69: 30 1.69 - 1.81: 56 Bond restraints: 13412 Sorted by residual: bond pdb=" C3' DG C 5 " pdb=" O3' DG C 5 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 9.75e+00 bond pdb=" C PRO B 475 " pdb=" O PRO B 475 " ideal model delta sigma weight residual 1.238 1.197 0.041 1.33e-02 5.65e+03 9.52e+00 bond pdb=" N VAL A 495 " pdb=" CA VAL A 495 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.14e-02 7.69e+03 8.63e+00 bond pdb=" C PRO A 475 " pdb=" O PRO A 475 " ideal model delta sigma weight residual 1.237 1.199 0.039 1.32e-02 5.74e+03 8.54e+00 bond pdb=" C3' DG D 8 " pdb=" C2' DG D 8 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.43e+00 ... (remaining 13407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 17789 2.07 - 4.15: 350 4.15 - 6.22: 41 6.22 - 8.30: 7 8.30 - 10.37: 1 Bond angle restraints: 18188 Sorted by residual: angle pdb=" N PRO A 468 " pdb=" CA PRO A 468 " pdb=" C PRO A 468 " ideal model delta sigma weight residual 111.32 121.69 -10.37 1.71e+00 3.42e-01 3.68e+01 angle pdb=" N PRO B 475 " pdb=" CA PRO B 475 " pdb=" C PRO B 475 " ideal model delta sigma weight residual 113.81 106.28 7.53 1.45e+00 4.76e-01 2.70e+01 angle pdb=" N ALA A 500 " pdb=" CA ALA A 500 " pdb=" C ALA A 500 " ideal model delta sigma weight residual 113.50 107.48 6.02 1.23e+00 6.61e-01 2.40e+01 angle pdb=" O4' DA D 7 " pdb=" C4' DA D 7 " pdb=" C3' DA D 7 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.17e+01 angle pdb=" N3 DT C 6 " pdb=" C4 DT C 6 " pdb=" O4 DT C 6 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 ... (remaining 18183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 7198 17.80 - 35.60: 635 35.60 - 53.39: 127 53.39 - 71.19: 42 71.19 - 88.99: 16 Dihedral angle restraints: 8018 sinusoidal: 3426 harmonic: 4592 Sorted by residual: dihedral pdb=" C GLU A 772 " pdb=" N GLU A 772 " pdb=" CA GLU A 772 " pdb=" CB GLU A 772 " ideal model delta harmonic sigma weight residual -122.60 -131.41 8.81 0 2.50e+00 1.60e-01 1.24e+01 dihedral pdb=" CA SER B 687 " pdb=" C SER B 687 " pdb=" N TYR B 688 " pdb=" CA TYR B 688 " ideal model delta harmonic sigma weight residual 180.00 162.66 17.34 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA TYR B 402 " pdb=" C TYR B 402 " pdb=" N MET B 403 " pdb=" CA MET B 403 " ideal model delta harmonic sigma weight residual 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 8015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1596 0.057 - 0.113: 300 0.113 - 0.170: 61 0.170 - 0.227: 15 0.227 - 0.283: 8 Chirality restraints: 1980 Sorted by residual: chirality pdb=" CA GLU A 772 " pdb=" N GLU A 772 " pdb=" C GLU A 772 " pdb=" CB GLU A 772 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" P DG C 2 " pdb=" OP1 DG C 2 " pdb=" OP2 DG C 2 " pdb=" O5' DG C 2 " both_signs ideal model delta sigma weight residual True 2.34 -2.62 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB VAL A 495 " pdb=" CA VAL A 495 " pdb=" CG1 VAL A 495 " pdb=" CG2 VAL A 495 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 1977 not shown) Planarity restraints: 2268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 490 " -0.055 5.00e-02 4.00e+02 8.46e-02 1.15e+01 pdb=" N PRO B 491 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO B 491 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 491 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 508 " 0.038 5.00e-02 4.00e+02 5.86e-02 5.50e+00 pdb=" N PRO B 509 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 509 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 509 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 508 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO A 509 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 509 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 509 " -0.031 5.00e-02 4.00e+02 ... (remaining 2265 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 169 2.65 - 3.21: 12059 3.21 - 3.78: 20242 3.78 - 4.34: 28397 4.34 - 4.90: 46971 Nonbonded interactions: 107838 Sorted by model distance: nonbonded pdb=" OH TYR A 179 " pdb=" OG SER A 303 " model vdw 2.089 3.040 nonbonded pdb=" OH TYR B 179 " pdb=" OG SER B 303 " model vdw 2.130 3.040 nonbonded pdb=" OE2 GLU A 692 " pdb=" OG SER B 687 " model vdw 2.175 3.040 nonbonded pdb=" O LYS B 160 " pdb=" OG1 THR B 172 " model vdw 2.206 3.040 nonbonded pdb=" NH1 ARG B 634 " pdb=" O ASP B 635 " model vdw 2.231 3.120 ... (remaining 107833 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.00 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: 2.550 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.700 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 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 : 0.005 0.044 13412 Z= 0.288 Angle : 0.681 10.375 18188 Z= 0.422 Chirality : 0.052 0.283 1980 Planarity : 0.004 0.085 2268 Dihedral : 14.903 88.988 5062 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.44 % Favored : 95.37 % Rotamer: Outliers : 0.36 % Allowed : 0.57 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.21), residues: 1554 helix: 1.41 (0.24), residues: 456 sheet: -0.34 (0.32), residues: 262 loop : -0.78 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 128 TYR 0.022 0.001 TYR A 9 PHE 0.024 0.002 PHE B 510 TRP 0.020 0.002 TRP B 214 HIS 0.008 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.29 (13412) covalent geometry : angle 0.68072 / 0.42 (18188) hydrogen bonds : bond 0.19460 / 12.56 ( 525) hydrogen bonds : angle 8.50188 / 5.99 ( 1473) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 250 time to evaluate : 0.488 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: A 185 LEU cc_start: 0.9211 (tp) cc_final: 0.8892 (tp) REVERT: B 448 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8558 (tp30) outliers start: 5 outliers final: 0 residues processed: 253 average time/residue: 0.1263 time to fit residues: 45.0526 Evaluate side-chains 129 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 HIS ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN ** B 406 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 = 0.4084 r_free = 0.4084 target = 0.105173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.073916 restraints weight = 48242.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.076355 restraints weight = 26793.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.078002 restraints weight = 19053.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.079005 restraints weight = 15505.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.079648 restraints weight = 13718.378| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13412 Z= 0.162 Angle : 0.691 10.477 18188 Z= 0.353 Chirality : 0.046 0.274 1980 Planarity : 0.005 0.057 2268 Dihedral : 9.036 71.221 1884 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.80 % Favored : 96.07 % Rotamer: Outliers : 0.86 % Allowed : 8.95 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.21), residues: 1554 helix: 1.13 (0.24), residues: 466 sheet: -0.07 (0.30), residues: 302 loop : -0.75 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 128 TYR 0.026 0.002 TYR B 9 PHE 0.016 0.002 PHE B 481 TRP 0.011 0.002 TRP A 131 HIS 0.009 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (13412) covalent geometry : angle 0.69134 / 0.35 (18188) hydrogen bonds : bond 0.05153 / 3.27 ( 525) hydrogen bonds : angle 6.69736 / 4.63 ( 1473) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.520 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: A 206 PHE cc_start: 0.9109 (m-80) cc_final: 0.8863 (m-80) REVERT: A 238 TYR cc_start: 0.8537 (m-80) cc_final: 0.8242 (m-80) REVERT: A 266 MET cc_start: 0.9289 (ptm) cc_final: 0.8529 (ppp) REVERT: A 368 MET cc_start: 0.8625 (ttm) cc_final: 0.8331 (tpp) REVERT: A 403 MET cc_start: 0.8325 (tpp) cc_final: 0.8046 (tpt) REVERT: A 493 LEU cc_start: 0.9491 (tp) cc_final: 0.9070 (pp) REVERT: A 549 TRP cc_start: 0.9043 (m100) cc_final: 0.8804 (m100) REVERT: A 729 MET cc_start: 0.8246 (ttm) cc_final: 0.7467 (mtp) REVERT: B 275 MET cc_start: 0.7240 (ppp) cc_final: 0.6744 (ppp) REVERT: B 368 MET cc_start: 0.8819 (ttm) cc_final: 0.8599 (ttm) REVERT: B 448 GLU cc_start: 0.9392 (mm-30) cc_final: 0.8832 (tp30) outliers start: 12 outliers final: 8 residues processed: 167 average time/residue: 0.1219 time to fit residues: 29.7316 Evaluate side-chains 127 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 71 optimal weight: 0.0060 chunk 119 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN A 242 ASN ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN B 406 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.104721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.073439 restraints weight = 48666.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.075980 restraints weight = 26918.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.077670 restraints weight = 19077.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.078721 restraints weight = 15496.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.079048 restraints weight = 13693.782| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13412 Z= 0.150 Angle : 0.640 12.976 18188 Z= 0.329 Chirality : 0.045 0.353 1980 Planarity : 0.004 0.053 2268 Dihedral : 9.136 70.807 1884 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.22 % Favored : 96.65 % Rotamer: Outliers : 1.36 % Allowed : 10.74 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.21), residues: 1554 helix: 1.34 (0.24), residues: 450 sheet: -0.24 (0.27), residues: 334 loop : -0.64 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 455 TYR 0.024 0.002 TYR B 562 PHE 0.027 0.001 PHE A 736 TRP 0.009 0.001 TRP A 131 HIS 0.011 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (13412) covalent geometry : angle 0.63969 / 0.33 (18188) hydrogen bonds : bond 0.04380 / 2.80 ( 525) hydrogen bonds : angle 6.22565 / 4.30 ( 1473) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.516 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 206 PHE cc_start: 0.9173 (m-80) cc_final: 0.8886 (m-80) REVERT: A 238 TYR cc_start: 0.8549 (m-80) cc_final: 0.8257 (m-80) REVERT: A 266 MET cc_start: 0.9210 (ptm) cc_final: 0.8539 (ppp) REVERT: A 403 MET cc_start: 0.8343 (tpp) cc_final: 0.8121 (tpt) REVERT: A 493 LEU cc_start: 0.9497 (tp) cc_final: 0.9093 (pp) REVERT: A 535 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9177 (tt) REVERT: A 549 TRP cc_start: 0.9083 (m100) cc_final: 0.8882 (m100) REVERT: A 729 MET cc_start: 0.8244 (ttm) cc_final: 0.7483 (mtp) REVERT: B 275 MET cc_start: 0.7359 (ppp) cc_final: 0.6872 (ppp) REVERT: B 448 GLU cc_start: 0.9412 (mm-30) cc_final: 0.8855 (tp30) outliers start: 19 outliers final: 8 residues processed: 136 average time/residue: 0.1172 time to fit residues: 23.7714 Evaluate side-chains 121 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 689 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 58 optimal weight: 4.9990 chunk 77 optimal weight: 0.0370 chunk 55 optimal weight: 0.3980 chunk 24 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 148 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.105106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.073770 restraints weight = 48610.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.076214 restraints weight = 27085.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.077909 restraints weight = 19120.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.078992 restraints weight = 15550.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.079365 restraints weight = 13693.647| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13412 Z= 0.128 Angle : 0.620 10.647 18188 Z= 0.316 Chirality : 0.044 0.225 1980 Planarity : 0.004 0.042 2268 Dihedral : 9.232 68.646 1884 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.15 % Favored : 96.72 % Rotamer: Outliers : 1.58 % Allowed : 11.75 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.21), residues: 1554 helix: 1.36 (0.25), residues: 450 sheet: -0.14 (0.27), residues: 334 loop : -0.57 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 433 TYR 0.021 0.001 TYR B 643 PHE 0.023 0.001 PHE B 481 TRP 0.008 0.001 TRP A 131 HIS 0.008 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (13412) covalent geometry : angle 0.62038 / 0.32 (18188) hydrogen bonds : bond 0.04038 / 2.60 ( 525) hydrogen bonds : angle 5.85935 / 4.04 ( 1473) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.451 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 175 LEU cc_start: 0.9021 (tt) cc_final: 0.8504 (mp) REVERT: A 206 PHE cc_start: 0.9231 (m-80) cc_final: 0.8894 (m-80) REVERT: A 238 TYR cc_start: 0.8556 (m-80) cc_final: 0.8277 (m-80) REVERT: A 275 MET cc_start: 0.6668 (pmm) cc_final: 0.5086 (pmm) REVERT: A 493 LEU cc_start: 0.9528 (tp) cc_final: 0.9113 (pp) REVERT: A 535 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9195 (tt) REVERT: A 729 MET cc_start: 0.8269 (ttm) cc_final: 0.7472 (mtp) REVERT: B 275 MET cc_start: 0.7370 (ppp) cc_final: 0.6824 (ppp) REVERT: B 448 GLU cc_start: 0.9411 (mm-30) cc_final: 0.8849 (tp30) REVERT: B 679 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.9159 (mp) REVERT: B 748 MET cc_start: 0.9338 (mmm) cc_final: 0.9132 (mmm) outliers start: 22 outliers final: 11 residues processed: 139 average time/residue: 0.1119 time to fit residues: 23.6660 Evaluate side-chains 125 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 689 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.102779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.071460 restraints weight = 49642.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.073896 restraints weight = 27507.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.075438 restraints weight = 19554.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.076484 restraints weight = 16105.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.076818 restraints weight = 14203.203| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 13412 Z= 0.199 Angle : 0.632 9.746 18188 Z= 0.325 Chirality : 0.044 0.206 1980 Planarity : 0.004 0.050 2268 Dihedral : 9.298 68.691 1884 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.35 % Favored : 96.53 % Rotamer: Outliers : 1.50 % Allowed : 13.25 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.21), residues: 1554 helix: 1.30 (0.24), residues: 456 sheet: -0.11 (0.27), residues: 336 loop : -0.61 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 455 TYR 0.016 0.001 TYR A 613 PHE 0.013 0.001 PHE A 736 TRP 0.010 0.002 TRP B 214 HIS 0.007 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 (13412) covalent geometry : angle 0.63238 / 0.33 (18188) hydrogen bonds : bond 0.03977 / 2.54 ( 525) hydrogen bonds : angle 5.72112 / 3.90 ( 1473) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.527 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 172 THR cc_start: 0.9314 (m) cc_final: 0.8878 (p) REVERT: A 175 LEU cc_start: 0.9053 (tt) cc_final: 0.8533 (mp) REVERT: A 206 PHE cc_start: 0.9213 (m-80) cc_final: 0.8863 (m-80) REVERT: A 238 TYR cc_start: 0.8545 (m-80) cc_final: 0.8289 (m-80) REVERT: A 266 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.7749 (ppp) REVERT: A 275 MET cc_start: 0.6683 (pmm) cc_final: 0.5163 (pmm) REVERT: A 493 LEU cc_start: 0.9524 (tp) cc_final: 0.9091 (pp) REVERT: A 535 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9252 (tt) REVERT: A 729 MET cc_start: 0.8298 (ttm) cc_final: 0.7539 (mtp) REVERT: B 275 MET cc_start: 0.7423 (ppp) cc_final: 0.6859 (ppp) REVERT: B 448 GLU cc_start: 0.9429 (mm-30) cc_final: 0.8889 (tp30) REVERT: B 748 MET cc_start: 0.9355 (mmm) cc_final: 0.9155 (mmm) outliers start: 21 outliers final: 12 residues processed: 125 average time/residue: 0.1158 time to fit residues: 21.9212 Evaluate side-chains 124 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 689 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 40 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 HIS B 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.103404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.072149 restraints weight = 48831.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.074583 restraints weight = 27272.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.076247 restraints weight = 19310.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.077270 restraints weight = 15697.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.077749 restraints weight = 13900.841| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13412 Z= 0.134 Angle : 0.614 13.452 18188 Z= 0.310 Chirality : 0.044 0.236 1980 Planarity : 0.004 0.046 2268 Dihedral : 9.342 68.292 1884 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.15 % Favored : 96.72 % Rotamer: Outliers : 1.58 % Allowed : 13.90 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.21), residues: 1554 helix: 1.30 (0.24), residues: 456 sheet: -0.09 (0.28), residues: 338 loop : -0.58 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 455 TYR 0.015 0.001 TYR B 562 PHE 0.014 0.001 PHE B 481 TRP 0.010 0.001 TRP B 214 HIS 0.007 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (13412) covalent geometry : angle 0.61354 / 0.31 (18188) hydrogen bonds : bond 0.03800 / 2.43 ( 525) hydrogen bonds : angle 5.54179 / 3.77 ( 1473) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.586 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 172 THR cc_start: 0.9310 (m) cc_final: 0.8915 (p) REVERT: A 175 LEU cc_start: 0.9024 (tt) cc_final: 0.8486 (mp) REVERT: A 206 PHE cc_start: 0.9222 (m-80) cc_final: 0.8855 (m-80) REVERT: A 238 TYR cc_start: 0.8547 (m-80) cc_final: 0.8292 (m-80) REVERT: A 493 LEU cc_start: 0.9530 (tp) cc_final: 0.9095 (pp) REVERT: A 541 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8914 (mm-30) REVERT: A 729 MET cc_start: 0.8235 (ttm) cc_final: 0.7487 (mtp) REVERT: A 740 MET cc_start: 0.8894 (tpp) cc_final: 0.8226 (mpp) REVERT: B 275 MET cc_start: 0.7342 (ppp) cc_final: 0.6836 (ppp) REVERT: B 322 PHE cc_start: 0.9256 (m-80) cc_final: 0.8895 (m-80) REVERT: B 352 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8594 (mt) REVERT: B 448 GLU cc_start: 0.9415 (mm-30) cc_final: 0.8882 (tp30) REVERT: B 489 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8572 (m-10) REVERT: B 679 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9187 (mp) outliers start: 22 outliers final: 12 residues processed: 126 average time/residue: 0.1188 time to fit residues: 22.4583 Evaluate side-chains 127 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 774 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 120 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 131 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 3 optimal weight: 0.1980 chunk 57 optimal weight: 0.5980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 HIS A 672 HIS A 746 GLN ** B 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.101734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.070764 restraints weight = 48922.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.073096 restraints weight = 27196.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.074687 restraints weight = 19321.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.075666 restraints weight = 15719.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.076114 restraints weight = 13924.237| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 13412 Z= 0.188 Angle : 0.634 14.064 18188 Z= 0.322 Chirality : 0.043 0.173 1980 Planarity : 0.004 0.045 2268 Dihedral : 9.458 68.841 1884 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.67 % Favored : 96.20 % Rotamer: Outliers : 1.79 % Allowed : 14.04 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.21), residues: 1554 helix: 1.33 (0.25), residues: 458 sheet: -0.24 (0.28), residues: 332 loop : -0.49 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 570 TYR 0.014 0.001 TYR B 562 PHE 0.019 0.001 PHE A 311 TRP 0.009 0.001 TRP B 214 HIS 0.010 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (13412) covalent geometry : angle 0.63377 / 0.32 (18188) hydrogen bonds : bond 0.03823 / 2.46 ( 525) hydrogen bonds : angle 5.52557 / 3.74 ( 1473) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.476 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 172 THR cc_start: 0.9312 (m) cc_final: 0.8935 (p) REVERT: A 206 PHE cc_start: 0.9217 (m-80) cc_final: 0.8837 (m-80) REVERT: A 238 TYR cc_start: 0.8567 (m-80) cc_final: 0.8318 (m-80) REVERT: A 266 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8552 (mtm) REVERT: A 275 MET cc_start: 0.6763 (pmm) cc_final: 0.5085 (pmm) REVERT: A 493 LEU cc_start: 0.9543 (tp) cc_final: 0.9115 (pp) REVERT: A 729 MET cc_start: 0.8297 (ttm) cc_final: 0.7558 (mtp) REVERT: A 740 MET cc_start: 0.8949 (tpp) cc_final: 0.8229 (mpp) REVERT: B 275 MET cc_start: 0.7010 (ppp) cc_final: 0.6369 (ppp) REVERT: B 352 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8598 (mt) REVERT: B 489 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8610 (m-10) REVERT: B 679 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9212 (mp) outliers start: 25 outliers final: 14 residues processed: 124 average time/residue: 0.1158 time to fit residues: 21.4939 Evaluate side-chains 123 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 689 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 12 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 746 GLN B 242 ASN ** B 758 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 = 0.4027 r_free = 0.4027 target = 0.100637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.069621 restraints weight = 49321.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.071976 restraints weight = 27417.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.073539 restraints weight = 19588.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.074412 restraints weight = 15985.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.074691 restraints weight = 14233.353| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 13412 Z= 0.210 Angle : 0.670 15.538 18188 Z= 0.336 Chirality : 0.044 0.152 1980 Planarity : 0.004 0.045 2268 Dihedral : 9.609 69.367 1884 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.60 % Favored : 96.27 % Rotamer: Outliers : 2.22 % Allowed : 14.54 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.21), residues: 1554 helix: 1.33 (0.24), residues: 458 sheet: -0.29 (0.29), residues: 332 loop : -0.50 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 570 TYR 0.022 0.001 TYR B 434 PHE 0.015 0.002 PHE B 481 TRP 0.012 0.002 TRP B 214 HIS 0.014 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (13412) covalent geometry : angle 0.66964 / 0.34 (18188) hydrogen bonds : bond 0.03757 / 2.42 ( 525) hydrogen bonds : angle 5.52623 / 3.74 ( 1473) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.454 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 172 THR cc_start: 0.9346 (m) cc_final: 0.8981 (p) REVERT: A 183 TYR cc_start: 0.9306 (m-10) cc_final: 0.8959 (m-80) REVERT: A 206 PHE cc_start: 0.9228 (m-80) cc_final: 0.8837 (m-80) REVERT: A 238 TYR cc_start: 0.8589 (m-80) cc_final: 0.8353 (m-80) REVERT: A 266 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8650 (mtm) REVERT: A 275 MET cc_start: 0.6903 (pmm) cc_final: 0.5230 (pmm) REVERT: A 493 LEU cc_start: 0.9565 (tp) cc_final: 0.9137 (pp) REVERT: A 729 MET cc_start: 0.8407 (ttm) cc_final: 0.7635 (mtp) REVERT: A 740 MET cc_start: 0.8992 (tpp) cc_final: 0.8244 (mpp) REVERT: B 76 MET cc_start: 0.6127 (ppp) cc_final: 0.5721 (ppp) REVERT: B 119 GLU cc_start: 0.8374 (tp30) cc_final: 0.8138 (tp30) REVERT: B 275 MET cc_start: 0.7185 (ppp) cc_final: 0.6625 (ppp) REVERT: B 352 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8585 (mt) REVERT: B 489 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8600 (m-10) REVERT: B 679 ILE cc_start: 0.9477 (OUTLIER) cc_final: 0.9222 (mp) outliers start: 31 outliers final: 20 residues processed: 123 average time/residue: 0.1135 time to fit residues: 20.8647 Evaluate side-chains 128 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 347 TRP Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 689 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 32 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 65 optimal weight: 0.0980 chunk 67 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.102703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.071629 restraints weight = 49138.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.074149 restraints weight = 27078.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.075769 restraints weight = 19086.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.076747 restraints weight = 15532.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.077288 restraints weight = 13764.758| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13412 Z= 0.121 Angle : 0.645 16.128 18188 Z= 0.319 Chirality : 0.044 0.317 1980 Planarity : 0.004 0.045 2268 Dihedral : 9.686 68.185 1884 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.22 % Favored : 96.65 % Rotamer: Outliers : 1.86 % Allowed : 14.54 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.21), residues: 1554 helix: 1.32 (0.24), residues: 458 sheet: -0.16 (0.29), residues: 324 loop : -0.48 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 369 TYR 0.014 0.001 TYR B 562 PHE 0.021 0.001 PHE B 26 TRP 0.010 0.001 TRP B 214 HIS 0.006 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (13412) covalent geometry : angle 0.64514 / 0.32 (18188) hydrogen bonds : bond 0.03653 / 2.38 ( 525) hydrogen bonds : angle 5.41283 / 3.65 ( 1473) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.463 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 172 THR cc_start: 0.9326 (m) cc_final: 0.8985 (p) REVERT: A 183 TYR cc_start: 0.9296 (m-10) cc_final: 0.8976 (m-80) REVERT: A 206 PHE cc_start: 0.9233 (m-80) cc_final: 0.8832 (m-80) REVERT: A 238 TYR cc_start: 0.8574 (m-80) cc_final: 0.8334 (m-80) REVERT: A 266 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8561 (mtm) REVERT: A 275 MET cc_start: 0.6844 (pmm) cc_final: 0.5174 (pmm) REVERT: A 493 LEU cc_start: 0.9528 (tp) cc_final: 0.9107 (pp) REVERT: A 541 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8971 (mm-30) REVERT: A 729 MET cc_start: 0.8328 (ttm) cc_final: 0.7606 (mtp) REVERT: A 740 MET cc_start: 0.8947 (tpp) cc_final: 0.8188 (mpp) REVERT: B 76 MET cc_start: 0.6037 (ppp) cc_final: 0.5638 (ppp) REVERT: B 275 MET cc_start: 0.7092 (ppp) cc_final: 0.6515 (ppp) REVERT: B 352 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8592 (mt) REVERT: B 454 HIS cc_start: 0.8629 (m-70) cc_final: 0.8401 (m-70) REVERT: B 489 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8568 (m-10) REVERT: B 679 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.9223 (mp) outliers start: 26 outliers final: 17 residues processed: 126 average time/residue: 0.0977 time to fit residues: 18.9538 Evaluate side-chains 130 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 347 TRP Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 8 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 chunk 96 optimal weight: 0.0980 chunk 81 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 26 optimal weight: 0.0770 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 overall best weight: 1.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.101833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.070956 restraints weight = 48875.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.073405 restraints weight = 27097.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.074943 restraints weight = 19090.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.075927 restraints weight = 15565.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.076420 restraints weight = 13792.579| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13412 Z= 0.150 Angle : 0.651 15.751 18188 Z= 0.320 Chirality : 0.043 0.194 1980 Planarity : 0.004 0.046 2268 Dihedral : 9.821 68.478 1884 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.54 % Favored : 96.33 % Rotamer: Outliers : 1.79 % Allowed : 14.76 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.21), residues: 1554 helix: 1.38 (0.24), residues: 458 sheet: -0.17 (0.29), residues: 322 loop : -0.46 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 98 TYR 0.014 0.001 TYR B 562 PHE 0.014 0.001 PHE B 481 TRP 0.010 0.001 TRP B 214 HIS 0.007 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (13412) covalent geometry : angle 0.65069 / 0.32 (18188) hydrogen bonds : bond 0.03568 / 2.31 ( 525) hydrogen bonds : angle 5.37123 / 3.62 ( 1473) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.613 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 172 THR cc_start: 0.9331 (m) cc_final: 0.8999 (p) REVERT: A 183 TYR cc_start: 0.9302 (m-10) cc_final: 0.8978 (m-80) REVERT: A 206 PHE cc_start: 0.9213 (m-80) cc_final: 0.8827 (m-80) REVERT: A 266 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8579 (mtm) REVERT: A 275 MET cc_start: 0.6817 (pmm) cc_final: 0.5152 (pmm) REVERT: A 493 LEU cc_start: 0.9531 (tp) cc_final: 0.9124 (pp) REVERT: A 541 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8968 (mm-30) REVERT: A 729 MET cc_start: 0.8325 (ttm) cc_final: 0.7684 (mtp) REVERT: A 740 MET cc_start: 0.8974 (tpp) cc_final: 0.8191 (mpp) REVERT: B 76 MET cc_start: 0.6065 (ppp) cc_final: 0.5728 (ppp) REVERT: B 275 MET cc_start: 0.7060 (ppp) cc_final: 0.6488 (ppp) REVERT: B 352 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8602 (mt) REVERT: B 370 ASP cc_start: 0.9045 (m-30) cc_final: 0.8803 (m-30) REVERT: B 454 HIS cc_start: 0.8613 (m-70) cc_final: 0.8380 (m-70) REVERT: B 489 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8596 (m-10) REVERT: B 579 LYS cc_start: 0.9356 (mmmt) cc_final: 0.9032 (mmmm) REVERT: B 679 ILE cc_start: 0.9478 (OUTLIER) cc_final: 0.9233 (mp) REVERT: B 729 MET cc_start: 0.7971 (tmm) cc_final: 0.6637 (tmm) outliers start: 25 outliers final: 18 residues processed: 124 average time/residue: 0.1077 time to fit residues: 20.6856 Evaluate side-chains 129 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 347 TRP Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 689 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 54 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 GLN B 168 HIS ** B 758 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 = 0.4022 r_free = 0.4022 target = 0.100270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.069528 restraints weight = 49583.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.071953 restraints weight = 27325.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.073475 restraints weight = 19373.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.074349 restraints weight = 15849.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.074613 restraints weight = 14141.906| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 13412 Z= 0.190 Angle : 0.658 14.641 18188 Z= 0.327 Chirality : 0.043 0.157 1980 Planarity : 0.004 0.046 2268 Dihedral : 10.130 68.467 1884 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.80 % Favored : 96.07 % Rotamer: Outliers : 1.72 % Allowed : 14.83 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.21), residues: 1554 helix: 1.40 (0.24), residues: 458 sheet: -0.23 (0.29), residues: 310 loop : -0.42 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 433 TYR 0.015 0.001 TYR B 562 PHE 0.016 0.001 PHE B 19 TRP 0.012 0.002 TRP B 214 HIS 0.006 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (13412) covalent geometry : angle 0.65828 / 0.33 (18188) hydrogen bonds : bond 0.03581 / 2.31 ( 525) hydrogen bonds : angle 5.42160 / 3.66 ( 1473) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2670.42 seconds wall clock time: 46 minutes 56.59 seconds (2816.59 seconds total)