Starting phenix.real_space_refine on Fri Jul 3 09:57:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wmf_66089/07_2026/9wmf_66089.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wmf_66089/07_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_66089/07_2026/9wmf_66089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wmf_66089/07_2026/9wmf_66089.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wmf_66089/07_2026/9wmf_66089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wmf_66089/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.05, per 1000 atoms: 0.16 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: 0.65 Conformation dependent library (CDL) restraints added in 415.1 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: 1.24 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: 1.76 Time building geometry restraints manager: 0.88 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: 17791 2.07 - 4.15: 348 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.920 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.830 ------------------------------------------------------------------------------- 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= 0.287 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 0.68060 / 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 : 0.312 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: 0.1109 time to fit residues: 38.9959 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 : 0.357 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.105137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.074087 restraints weight = 48084.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.076511 restraints weight = 26672.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.078186 restraints weight = 18924.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.079204 restraints weight = 15344.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.079628 restraints weight = 13547.354| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1969 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 : 0.695 10.496 18188 Z= 0.354 Chirality : 0.046 0.260 1980 Planarity : 0.005 0.057 2268 Dihedral : 9.050 71.359 1884 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.80 % Favored : 96.07 % Rotamer: Outliers : 0.86 % Allowed : 8.88 % Favored : 90.26 % 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: 1.12 (0.24), residues: 466 sheet: -0.08 (0.30), residues: 302 loop : -0.77 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 522 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 0.012 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (13412) covalent geometry : angle 0.69482 / 0.35 (18188) hydrogen bonds : bond 0.05094 / 3.22 ( 525) hydrogen bonds : angle 6.69857 / 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 172 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.569 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: 0.9118 (m-80) cc_final: 0.8883 (m-80) REVERT: A 238 TYR cc_start: 0.8541 (m-80) cc_final: 0.8246 (m-80) REVERT: A 266 MET cc_start: 0.9307 (ptm) cc_final: 0.8530 (ppp) REVERT: A 368 MET cc_start: 0.8633 (ttm) cc_final: 0.8340 (tpp) REVERT: A 403 MET cc_start: 0.8322 (tpp) cc_final: 0.8049 (tpt) REVERT: A 493 LEU cc_start: 0.9485 (tp) cc_final: 0.9068 (pp) REVERT: A 549 TRP cc_start: 0.9042 (m100) cc_final: 0.8802 (m100) REVERT: B 275 MET cc_start: 0.7230 (ppp) cc_final: 0.6750 (ppp) REVERT: B 448 GLU cc_start: 0.9393 (mm-30) cc_final: 0.8838 (tp30) outliers start: 12 outliers final: 8 residues processed: 168 average time/residue: 0.1210 time to fit residues: 29.6427 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 : 0.480 ------------------------------------------------------------------------------- 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: 2.9990 chunk 119 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 139 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.104666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.073485 restraints weight = 48684.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.076003 restraints weight = 26870.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.077666 restraints weight = 19023.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.078709 restraints weight = 15467.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.079200 restraints weight = 13683.039| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13412 Z= 0.146 Angle : 0.638 12.804 18188 Z= 0.326 Chirality : 0.045 0.195 1980 Planarity : 0.004 0.046 2268 Dihedral : 9.169 70.858 1884 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.28 % Favored : 96.59 % Rotamer: Outliers : 1.36 % Allowed : 11.03 % Favored : 87.61 % 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: -0.01 (0.21), residues: 1554 helix: 1.33 (0.24), residues: 450 sheet: -0.26 (0.27), residues: 334 loop : -0.64 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 455 TYR 0.025 0.002 TYR B 562 PHE 0.028 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 0.00321 / 0.15 (13412) covalent geometry : angle 0.63783 / 0.33 (18188) hydrogen bonds : bond 0.04396 / 2.81 ( 525) hydrogen bonds : angle 6.19791 / 4.28 ( 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 147 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.313 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 175 LEU cc_start: 0.9083 (tt) cc_final: 0.8568 (mp) REVERT: A 206 PHE cc_start: 0.9182 (m-80) cc_final: 0.8898 (m-80) REVERT: A 238 TYR cc_start: 0.8547 (m-80) cc_final: 0.8258 (m-80) REVERT: A 266 MET cc_start: 0.9207 (ptm) cc_final: 0.8535 (ppp) REVERT: A 403 MET cc_start: 0.8335 (tpp) cc_final: 0.8122 (tpt) REVERT: A 418 LEU cc_start: 0.9566 (tt) cc_final: 0.9286 (tt) REVERT: A 451 LYS cc_start: 0.9732 (ptpt) cc_final: 0.9419 (ptpp) REVERT: A 493 LEU cc_start: 0.9496 (tp) cc_final: 0.9092 (pp) REVERT: A 535 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9179 (tt) REVERT: A 549 TRP cc_start: 0.9087 (m100) cc_final: 0.8884 (m100) REVERT: A 729 MET cc_start: 0.7767 (ttm) cc_final: 0.7334 (mtp) REVERT: B 275 MET cc_start: 0.7360 (ppp) cc_final: 0.6875 (ppp) REVERT: B 448 GLU cc_start: 0.9410 (mm-30) cc_final: 0.8854 (tp30) outliers start: 19 outliers final: 8 residues processed: 137 average time/residue: 0.1050 time to fit residues: 21.4136 Evaluate side-chains 122 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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: 5.9990 chunk 77 optimal weight: 0.2980 chunk 55 optimal weight: 0.2980 chunk 24 optimal weight: 0.2980 chunk 59 optimal weight: 0.0870 chunk 86 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.104729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.073425 restraints weight = 48621.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.075952 restraints weight = 26861.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.077589 restraints weight = 18981.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.078604 restraints weight = 15466.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.079261 restraints weight = 13689.612| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2771 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= 0.131 Angle : 0.611 9.952 18188 Z= 0.313 Chirality : 0.044 0.170 1980 Planarity : 0.004 0.044 2268 Dihedral : 9.237 68.920 1884 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.09 % Favored : 96.78 % Rotamer: Outliers : 1.65 % Allowed : 12.11 % Favored : 86.25 % 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: 1.34 (0.24), residues: 452 sheet: -0.15 (0.27), residues: 334 loop : -0.55 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 455 TYR 0.028 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 0.00289 / 0.13 (13412) covalent geometry : angle 0.61075 / 0.31 (18188) hydrogen bonds : bond 0.04041 / 2.59 ( 525) hydrogen bonds : angle 5.88845 / 4.06 ( 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 145 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.9049 (tt) cc_final: 0.8536 (mp) REVERT: A 206 PHE cc_start: 0.9231 (m-80) cc_final: 0.8900 (m-80) REVERT: A 238 TYR cc_start: 0.8533 (m-80) cc_final: 0.8264 (m-80) REVERT: A 275 MET cc_start: 0.6653 (pmm) cc_final: 0.5074 (pmm) REVERT: A 418 LEU cc_start: 0.9586 (tt) cc_final: 0.9279 (tt) REVERT: A 493 LEU cc_start: 0.9510 (tp) cc_final: 0.9088 (pp) REVERT: A 535 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9131 (tt) REVERT: A 539 VAL cc_start: 0.9475 (OUTLIER) cc_final: 0.9248 (p) REVERT: A 729 MET cc_start: 0.7953 (ttm) cc_final: 0.7439 (mtp) REVERT: B 275 MET cc_start: 0.7329 (ppp) cc_final: 0.6881 (ppp) REVERT: B 311 PHE cc_start: 0.9047 (m-80) cc_final: 0.8820 (m-80) REVERT: B 448 GLU cc_start: 0.9416 (mm-30) cc_final: 0.8850 (tp30) REVERT: B 679 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9137 (mp) outliers start: 23 outliers final: 12 residues processed: 135 average time/residue: 0.1049 time to fit residues: 21.2562 Evaluate side-chains 126 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 540 LEU 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 159 TYR 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 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: 0.6980 chunk 39 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** B 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.102514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.071113 restraints weight = 49418.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.073626 restraints weight = 27250.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.075189 restraints weight = 19305.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.076161 restraints weight = 15751.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.076759 restraints weight = 13990.914| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 13412 Z= 0.192 Angle : 0.627 12.650 18188 Z= 0.324 Chirality : 0.044 0.200 1980 Planarity : 0.004 0.053 2268 Dihedral : 9.338 68.705 1884 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 1.72 % Allowed : 13.04 % 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: 0.13 (0.21), residues: 1554 helix: 1.42 (0.25), residues: 456 sheet: -0.13 (0.28), residues: 336 loop : -0.58 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 455 TYR 0.018 0.001 TYR B 643 PHE 0.020 0.001 PHE B 481 TRP 0.012 0.002 TRP A 549 HIS 0.009 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (13412) covalent geometry : angle 0.62746 / 0.32 (18188) hydrogen bonds : bond 0.03967 / 2.53 ( 525) hydrogen bonds : angle 5.68759 / 3.87 ( 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 139 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 THR cc_start: 0.9304 (m) cc_final: 0.8879 (p) REVERT: A 175 LEU cc_start: 0.9074 (tt) cc_final: 0.8550 (mp) REVERT: A 206 PHE cc_start: 0.9223 (m-80) cc_final: 0.8874 (m-80) REVERT: A 238 TYR cc_start: 0.8530 (m-80) cc_final: 0.8283 (m-80) REVERT: A 266 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.7789 (ppp) REVERT: A 275 MET cc_start: 0.6649 (pmm) cc_final: 0.5062 (pmm) REVERT: A 418 LEU cc_start: 0.9593 (tt) cc_final: 0.9328 (tt) REVERT: A 493 LEU cc_start: 0.9517 (tp) cc_final: 0.9096 (pp) REVERT: A 535 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9242 (tt) REVERT: A 539 VAL cc_start: 0.9484 (OUTLIER) cc_final: 0.9266 (p) REVERT: A 729 MET cc_start: 0.8013 (ttm) cc_final: 0.7607 (mtp) REVERT: A 740 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8094 (mpp) REVERT: B 275 MET cc_start: 0.7011 (ppp) cc_final: 0.6402 (ppp) REVERT: B 311 PHE cc_start: 0.9157 (m-80) cc_final: 0.8915 (m-80) REVERT: B 352 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8613 (mt) REVERT: B 448 GLU cc_start: 0.9434 (mm-30) cc_final: 0.8896 (tp30) REVERT: B 679 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.9192 (mp) outliers start: 24 outliers final: 12 residues processed: 128 average time/residue: 0.1082 time to fit residues: 21.4336 Evaluate side-chains 130 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 539 VAL Chi-restraints excluded: chain A residue 540 LEU 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 40 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 672 HIS A 746 GLN ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4032 r_free = 0.4032 target = 0.101223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.070164 restraints weight = 49252.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.072571 restraints weight = 27172.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.074130 restraints weight = 19284.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.075066 restraints weight = 15756.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.075391 restraints weight = 14014.647| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 13412 Z= 0.202 Angle : 0.628 12.665 18188 Z= 0.321 Chirality : 0.044 0.331 1980 Planarity : 0.004 0.047 2268 Dihedral : 9.440 68.878 1884 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.28 % Favored : 96.59 % Rotamer: Outliers : 2.15 % Allowed : 13.61 % Favored : 84.24 % 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: 0.13 (0.21), residues: 1554 helix: 1.40 (0.25), residues: 456 sheet: -0.21 (0.29), residues: 320 loop : -0.53 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 455 TYR 0.016 0.001 TYR B 562 PHE 0.018 0.002 PHE A 716 TRP 0.011 0.002 TRP B 214 HIS 0.006 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (13412) covalent geometry : angle 0.62824 / 0.32 (18188) hydrogen bonds : bond 0.03892 / 2.50 ( 525) hydrogen bonds : angle 5.60715 / 3.81 ( 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 141 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 THR cc_start: 0.9322 (m) cc_final: 0.8919 (p) REVERT: A 175 LEU cc_start: 0.9121 (tt) cc_final: 0.8572 (mp) REVERT: A 206 PHE cc_start: 0.9226 (m-80) cc_final: 0.8861 (m-80) REVERT: A 238 TYR cc_start: 0.8569 (m-80) cc_final: 0.8322 (m-80) REVERT: A 418 LEU cc_start: 0.9600 (tt) cc_final: 0.9329 (tt) REVERT: A 493 LEU cc_start: 0.9553 (tp) cc_final: 0.9119 (pp) REVERT: A 535 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9247 (tt) REVERT: A 539 VAL cc_start: 0.9493 (OUTLIER) cc_final: 0.9275 (p) REVERT: B 275 MET cc_start: 0.7110 (ppp) cc_final: 0.6530 (ppp) REVERT: B 311 PHE cc_start: 0.9200 (m-80) cc_final: 0.8920 (m-80) REVERT: B 448 GLU cc_start: 0.9437 (mm-30) cc_final: 0.8914 (tp30) REVERT: B 489 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8679 (m-10) REVERT: B 679 ILE cc_start: 0.9464 (OUTLIER) cc_final: 0.9245 (mp) outliers start: 30 outliers final: 21 residues processed: 127 average time/residue: 0.1114 time to fit residues: 21.7766 Evaluate side-chains 126 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 539 VAL 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 5 ILE Chi-restraints excluded: chain B residue 6 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 171 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 347 TRP 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 662 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 120 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 104 optimal weight: 0.0670 chunk 3 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 HIS A 746 GLN B 406 ASN ** B 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4046 r_free = 0.4046 target = 0.101875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.070833 restraints weight = 48914.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.073251 restraints weight = 27127.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.074884 restraints weight = 19259.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.075827 restraints weight = 15636.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.076413 restraints weight = 13865.947| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13412 Z= 0.154 Angle : 0.621 14.518 18188 Z= 0.314 Chirality : 0.043 0.192 1980 Planarity : 0.004 0.046 2268 Dihedral : 9.503 68.777 1884 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.67 % Favored : 96.20 % Rotamer: Outliers : 2.29 % Allowed : 14.33 % Favored : 83.38 % 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: 1.37 (0.24), residues: 458 sheet: -0.20 (0.29), residues: 320 loop : -0.50 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 570 TYR 0.015 0.001 TYR B 562 PHE 0.018 0.001 PHE A 311 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 0.00338 / 0.15 (13412) covalent geometry : angle 0.62115 / 0.31 (18188) hydrogen bonds : bond 0.03765 / 2.43 ( 525) hydrogen bonds : angle 5.51566 / 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 142 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.543 Fit side-chains 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: 0.8937 (p) REVERT: A 206 PHE cc_start: 0.9225 (m-80) cc_final: 0.8857 (m-80) REVERT: A 238 TYR cc_start: 0.8559 (m-80) cc_final: 0.8317 (m-80) REVERT: A 266 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.7758 (ppp) REVERT: A 275 MET cc_start: 0.6850 (pmm) cc_final: 0.5128 (pmm) REVERT: A 418 LEU cc_start: 0.9585 (tt) cc_final: 0.9312 (tt) REVERT: A 493 LEU cc_start: 0.9530 (tp) cc_final: 0.9089 (pp) REVERT: A 535 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9230 (tt) REVERT: A 539 VAL cc_start: 0.9481 (OUTLIER) cc_final: 0.9245 (p) REVERT: A 740 MET cc_start: 0.9006 (tpp) cc_final: 0.8734 (tpp) REVERT: B 275 MET cc_start: 0.7052 (ppp) cc_final: 0.6425 (ppp) REVERT: B 311 PHE cc_start: 0.9203 (m-80) cc_final: 0.8878 (m-80) REVERT: B 352 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8595 (mt) REVERT: B 448 GLU cc_start: 0.9427 (mm-30) cc_final: 0.8905 (tp30) REVERT: B 489 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8641 (m-10) REVERT: B 729 MET cc_start: 0.7893 (tmm) cc_final: 0.6329 (tmm) outliers start: 32 outliers final: 19 residues processed: 126 average time/residue: 0.1011 time to fit residues: 20.0884 Evaluate side-chains 130 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 535 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 568 HIS 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 465 VAL 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 662 ASP Chi-restraints excluded: chain B residue 673 LYS 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: 7.9990 chunk 36 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 13 optimal weight: 0.0030 chunk 54 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 HIS ** B 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.101615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.070722 restraints weight = 48886.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.073173 restraints weight = 26866.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.074735 restraints weight = 19093.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.075708 restraints weight = 15580.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.076273 restraints weight = 13807.127| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3442 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= 0.157 Angle : 0.631 15.229 18188 Z= 0.316 Chirality : 0.044 0.297 1980 Planarity : 0.004 0.051 2268 Dihedral : 9.587 68.816 1884 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.54 % Favored : 96.33 % Rotamer: Outliers : 2.44 % Allowed : 14.40 % Favored : 83.17 % 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: 0.14 (0.21), residues: 1554 helix: 1.38 (0.24), residues: 458 sheet: -0.23 (0.29), residues: 322 loop : -0.49 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 433 TYR 0.014 0.001 TYR B 562 PHE 0.021 0.001 PHE A 736 TRP 0.009 0.001 TRP B 214 HIS 0.007 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (13412) covalent geometry : angle 0.63067 / 0.32 (18188) hydrogen bonds : bond 0.03724 / 2.41 ( 525) hydrogen bonds : angle 5.46580 / 3.69 ( 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 142 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 THR cc_start: 0.9328 (m) cc_final: 0.8957 (p) REVERT: A 206 PHE cc_start: 0.9227 (m-80) cc_final: 0.8849 (m-80) REVERT: A 238 TYR cc_start: 0.8567 (m-80) cc_final: 0.8334 (m-80) REVERT: A 275 MET cc_start: 0.6840 (pmm) cc_final: 0.5170 (pmm) REVERT: A 418 LEU cc_start: 0.9581 (tt) cc_final: 0.9310 (tt) REVERT: A 493 LEU cc_start: 0.9508 (tp) cc_final: 0.9097 (pp) REVERT: A 535 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9234 (tt) REVERT: A 539 VAL cc_start: 0.9473 (OUTLIER) cc_final: 0.9236 (p) REVERT: A 740 MET cc_start: 0.9035 (tpp) cc_final: 0.8293 (mpp) REVERT: B 76 MET cc_start: 0.5894 (ppp) cc_final: 0.5496 (ppp) REVERT: B 275 MET cc_start: 0.7045 (ppp) cc_final: 0.6451 (ppp) REVERT: B 311 PHE cc_start: 0.9212 (m-80) cc_final: 0.8829 (m-80) REVERT: B 322 PHE cc_start: 0.9355 (m-80) cc_final: 0.8976 (m-80) REVERT: B 352 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8597 (mt) REVERT: B 489 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8625 (m-10) outliers start: 34 outliers final: 24 residues processed: 126 average time/residue: 0.1039 time to fit residues: 20.4014 Evaluate side-chains 132 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 5 ILE 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 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 465 VAL 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 662 ASP Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 32 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 136 optimal weight: 0.0050 chunk 49 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 65 optimal weight: 0.4980 chunk 67 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 482 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.102450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.071559 restraints weight = 48872.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.073943 restraints weight = 27055.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.075586 restraints weight = 19077.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.076505 restraints weight = 15465.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.077167 restraints weight = 13741.147| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13412 Z= 0.128 Angle : 0.631 16.126 18188 Z= 0.315 Chirality : 0.044 0.196 1980 Planarity : 0.004 0.049 2268 Dihedral : 9.649 68.451 1884 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.60 % Favored : 96.27 % Rotamer: Outliers : 1.86 % Allowed : 14.83 % Favored : 83.31 % 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: 0.15 (0.21), residues: 1554 helix: 1.39 (0.24), residues: 458 sheet: -0.20 (0.29), residues: 322 loop : -0.49 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 570 TYR 0.020 0.001 TYR B 434 PHE 0.020 0.001 PHE A 736 TRP 0.009 0.001 TRP B 214 HIS 0.021 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (13412) covalent geometry : angle 0.63129 / 0.31 (18188) hydrogen bonds : bond 0.03673 / 2.38 ( 525) hydrogen bonds : angle 5.44363 / 3.66 ( 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 140 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 THR cc_start: 0.9322 (m) cc_final: 0.8971 (p) REVERT: A 183 TYR cc_start: 0.9294 (m-10) cc_final: 0.8961 (m-80) REVERT: A 206 PHE cc_start: 0.9224 (m-80) cc_final: 0.8842 (m-80) REVERT: A 238 TYR cc_start: 0.8563 (m-80) cc_final: 0.8325 (m-80) REVERT: A 275 MET cc_start: 0.6793 (pmm) cc_final: 0.5126 (pmm) REVERT: A 418 LEU cc_start: 0.9568 (tt) cc_final: 0.9292 (tt) REVERT: A 493 LEU cc_start: 0.9510 (tp) cc_final: 0.9075 (pp) REVERT: A 535 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9198 (tt) REVERT: A 539 VAL cc_start: 0.9470 (OUTLIER) cc_final: 0.9232 (p) REVERT: A 729 MET cc_start: 0.8487 (mtp) cc_final: 0.8226 (mtt) REVERT: A 740 MET cc_start: 0.9037 (tpp) cc_final: 0.8289 (mpp) REVERT: B 76 MET cc_start: 0.5936 (ppp) cc_final: 0.5601 (ppp) REVERT: B 275 MET cc_start: 0.7022 (ppp) cc_final: 0.6408 (ppp) REVERT: B 311 PHE cc_start: 0.9232 (m-80) cc_final: 0.8819 (m-80) REVERT: B 352 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8596 (mt) REVERT: B 454 HIS cc_start: 0.8667 (m-70) cc_final: 0.8454 (m-70) REVERT: B 489 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8606 (m-10) REVERT: B 729 MET cc_start: 0.7883 (tmm) cc_final: 0.6622 (tmm) outliers start: 26 outliers final: 19 residues processed: 127 average time/residue: 0.1116 time to fit residues: 21.5467 Evaluate side-chains 131 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 539 VAL 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 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: 9.9990 chunk 28 optimal weight: 20.0000 chunk 115 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 104 optimal weight: 0.7980 chunk 27 optimal weight: 0.0270 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 overall best weight: 1.5644 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.101774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.070928 restraints weight = 49029.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.073367 restraints weight = 26901.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.074922 restraints weight = 19024.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.075808 restraints weight = 15518.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.076422 restraints weight = 13812.567| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13412 Z= 0.152 Angle : 0.633 15.739 18188 Z= 0.315 Chirality : 0.043 0.166 1980 Planarity : 0.004 0.049 2268 Dihedral : 9.796 68.639 1884 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.67 % Favored : 96.20 % Rotamer: Outliers : 1.72 % Allowed : 14.97 % Favored : 83.31 % 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: 0.17 (0.21), residues: 1554 helix: 1.43 (0.24), residues: 458 sheet: -0.20 (0.29), residues: 322 loop : -0.49 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 98 TYR 0.016 0.001 TYR B 434 PHE 0.017 0.001 PHE A 736 TRP 0.010 0.001 TRP B 214 HIS 0.005 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (13412) covalent geometry : angle 0.63261 / 0.32 (18188) hydrogen bonds : bond 0.03592 / 2.32 ( 525) hydrogen bonds : angle 5.41315 / 3.64 ( 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 128 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.513 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: 0.9318 (m) cc_final: 0.8978 (p) REVERT: A 183 TYR cc_start: 0.9303 (m-10) cc_final: 0.8979 (m-80) REVERT: A 206 PHE cc_start: 0.9204 (m-80) cc_final: 0.8839 (m-80) REVERT: A 275 MET cc_start: 0.6830 (pmm) cc_final: 0.5159 (pmm) REVERT: A 418 LEU cc_start: 0.9571 (tt) cc_final: 0.9299 (tt) REVERT: A 493 LEU cc_start: 0.9510 (tp) cc_final: 0.9102 (pp) REVERT: A 535 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9217 (tt) REVERT: A 539 VAL cc_start: 0.9468 (OUTLIER) cc_final: 0.9230 (p) REVERT: A 729 MET cc_start: 0.8502 (mtp) cc_final: 0.8267 (mtt) REVERT: A 740 MET cc_start: 0.9068 (tpp) cc_final: 0.8309 (mpp) REVERT: B 76 MET cc_start: 0.6020 (ppp) cc_final: 0.5747 (ppp) REVERT: B 275 MET cc_start: 0.7083 (ppp) cc_final: 0.6480 (ppp) REVERT: B 311 PHE cc_start: 0.9267 (m-80) cc_final: 0.8870 (m-80) REVERT: B 352 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8600 (mt) REVERT: B 454 HIS cc_start: 0.8639 (m-70) cc_final: 0.8419 (m-70) REVERT: B 489 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8600 (m-10) REVERT: B 748 MET cc_start: 0.9268 (mmm) cc_final: 0.9044 (mmm) outliers start: 24 outliers final: 18 residues processed: 116 average time/residue: 0.1100 time to fit residues: 19.7107 Evaluate side-chains 125 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 479 LYS 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 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 368 MET 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 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: 0.9980 chunk 153 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 116 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.102305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.071757 restraints weight = 48587.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.074198 restraints weight = 26690.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.075797 restraints weight = 18811.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.076758 restraints weight = 15280.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.077113 restraints weight = 13517.086| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13412 Z= 0.128 Angle : 0.624 15.974 18188 Z= 0.308 Chirality : 0.043 0.173 1980 Planarity : 0.004 0.048 2268 Dihedral : 10.000 68.397 1884 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.54 % Favored : 96.33 % Rotamer: Outliers : 1.79 % Allowed : 14.90 % Favored : 83.31 % 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: 1.45 (0.24), residues: 458 sheet: -0.17 (0.29), residues: 322 loop : -0.47 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 455 TYR 0.014 0.001 TYR B 562 PHE 0.029 0.001 PHE B 19 TRP 0.010 0.001 TRP B 214 HIS 0.005 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (13412) covalent geometry : angle 0.62440 / 0.31 (18188) hydrogen bonds : bond 0.03522 / 2.29 ( 525) hydrogen bonds : angle 5.34421 / 3.61 ( 1473) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2687.40 seconds wall clock time: 47 minutes 17.26 seconds (2837.26 seconds total)