Starting phenix.real_space_refine on Thu Jun 4 13:58:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wmf_66089/06_2026/9wmf_66089.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wmf_66089/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9wmf_66089/06_2026/9wmf_66089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wmf_66089/06_2026/9wmf_66089.map" model { file = "/net/cci-nas-00/data/ceres_data/9wmf_66089/06_2026/9wmf_66089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wmf_66089/06_2026/9wmf_66089.cif" } 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-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13068 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6363 Classifications: {'peptide': 779} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 745} Chain: "C" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 171 Classifications: {'DNA': 8} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 7} Chain: "B" Number of atoms: 6363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6363 Classifications: {'peptide': 779} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 745} Chain: "D" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 171 Classifications: {'DNA': 8} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 7} Time building chain proxies: 3.39, per 1000 atoms: 0.26 Number of scatterers: 13068 At special positions: 0 Unit cell: (127.1, 127.1, 89.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 16 15.00 O 2392 8.00 N 2222 7.00 C 8406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 536.0 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: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 34 through 54 Processing helix chain 'A' and resid 105 through 126 removed outlier: 3.959A pdb=" N ASP A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL A 111 " --> pdb=" O HIS A 107 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 removed outlier: 4.139A pdb=" N TYR A 188 " --> pdb=" O CYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 199 through 202 removed outlier: 3.947A pdb=" N LYS A 202 " --> pdb=" O ASN A 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 199 through 202' Processing helix chain 'A' and resid 240 through 250 removed outlier: 4.286A pdb=" N HIS A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.503A pdb=" N SER A 298 " --> pdb=" O ARG A 295 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS A 300 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR A 301 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 302 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 370 through 383 removed outlier: 3.805A pdb=" N LYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE A 379 " --> pdb=" O ARG A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 423 Processing helix chain 'A' and resid 441 through 457 Processing helix chain 'A' and resid 474 through 490 removed outlier: 4.146A pdb=" N LYS A 486 " --> pdb=" O HIS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 527 through 546 Processing helix chain 'A' and resid 604 through 620 removed outlier: 4.202A pdb=" N LEU A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 656 Processing helix chain 'A' and resid 735 through 748 Processing helix chain 'A' and resid 761 through 771 removed outlier: 3.931A pdb=" N ILE A 767 " --> pdb=" O ILE A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 775 Processing helix chain 'B' and resid 34 through 54 Processing helix chain 'B' and resid 105 through 126 removed outlier: 4.001A pdb=" N ASP B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL B 111 " --> pdb=" O HIS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 188 Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 199 through 202 removed outlier: 4.107A pdb=" N LYS B 202 " --> pdb=" O ASN B 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 199 through 202' Processing helix chain 'B' and resid 240 through 250 removed outlier: 4.178A pdb=" N HIS B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 removed outlier: 4.139A pdb=" N ARG B 257 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 298 Processing helix chain 'B' and resid 299 through 304 removed outlier: 4.031A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE B 304 " --> pdb=" O HIS B 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 299 through 304' Processing helix chain 'B' and resid 306 through 322 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 370 through 383 removed outlier: 3.555A pdb=" N LYS B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE B 379 " --> pdb=" O ARG B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 423 Processing helix chain 'B' and resid 441 through 457 Processing helix chain 'B' and resid 474 through 489 removed outlier: 3.540A pdb=" N LEU B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 486 " --> pdb=" O HIS B 482 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 527 through 546 Processing helix chain 'B' and resid 604 through 620 removed outlier: 4.214A pdb=" N LEU B 608 " --> pdb=" O ARG B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 656 Processing helix chain 'B' and resid 735 through 748 Processing helix chain 'B' and resid 761 through 772 removed outlier: 4.104A pdb=" N ILE B 767 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU B 772 " --> pdb=" O ASP B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 775 No H-bonds generated for 'chain 'B' and resid 773 through 775' Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 10 removed outlier: 5.476A pdb=" N GLU A 155 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 62 removed outlier: 5.384A pdb=" N PHE A 66 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE A 26 " --> pdb=" O PHE A 66 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 68 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TYR A 21 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU A 95 " --> pdb=" O TYR A 21 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU A 23 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 79 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 278 through 281 removed outlier: 4.702A pdb=" N LYS A 224 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N SER A 267 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N PHE A 222 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N THR A 269 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU A 220 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 230 through 233 Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 327 Processing sheet with id=AA7, first strand: chain 'A' and resid 358 through 359 Processing sheet with id=AA8, first strand: chain 'A' and resid 430 through 434 Processing sheet with id=AA9, first strand: chain 'A' and resid 466 through 467 Processing sheet with id=AB1, first strand: chain 'A' and resid 507 through 510 Processing sheet with id=AB2, first strand: chain 'A' and resid 583 through 590 removed outlier: 4.658A pdb=" N GLN A 583 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 578 " --> pdb=" O GLN A 583 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE A 561 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL A 633 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 563 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP A 635 " --> pdb=" O ILE A 563 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE A 565 " --> pdb=" O ASP A 635 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE A 630 " --> pdb=" O GLY A 667 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL A 669 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE A 632 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU A 671 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ARG A 634 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N TYR A 666 " --> pdb=" O GLY A 732 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY A 732 " --> pdb=" O TYR A 666 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 668 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 726 " --> pdb=" O HIS A 672 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLU A 706 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER A 698 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AB4, first strand: chain 'B' and resid 8 through 10 Processing sheet with id=AB5, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.537A pdb=" N ALA B 69 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N PHE B 66 " --> pdb=" O PHE B 26 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N PHE B 26 " --> pdb=" O PHE B 66 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 68 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 70 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR B 21 " --> pdb=" O GLU B 95 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLU B 95 " --> pdb=" O TYR B 21 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU B 23 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 79 " --> pdb=" O ILE B 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 130 through 132 removed outlier: 5.311A pdb=" N GLU B 155 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 278 through 281 removed outlier: 4.602A pdb=" N SER B 265 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY B 221 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR B 269 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU B 219 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 230 through 233 Processing sheet with id=AB9, first strand: chain 'B' and resid 326 through 327 Processing sheet with id=AC1, first strand: chain 'B' and resid 358 through 359 removed outlier: 3.903A pdb=" N LEU B 351 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 430 through 434 Processing sheet with id=AC3, first strand: chain 'B' and resid 466 through 467 Processing sheet with id=AC4, first strand: chain 'B' and resid 507 through 511 removed outlier: 3.561A pdb=" N LYS B 508 " --> pdb=" O ARG B 522 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG B 522 " --> pdb=" O LYS B 508 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 583 through 586 removed outlier: 4.669A pdb=" N GLN B 583 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 578 " --> pdb=" O GLN B 583 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 583 through 586 removed outlier: 4.669A pdb=" N GLN B 583 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 578 " --> pdb=" O GLN B 583 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 565 " --> pdb=" O VAL B 633 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL B 567 " --> pdb=" O ASP B 635 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 630 " --> pdb=" O GLY B 667 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL B 669 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ILE B 632 " --> pdb=" O VAL B 669 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 671 " --> pdb=" O ILE B 632 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ARG B 634 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TYR B 666 " --> pdb=" O GLY B 732 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLY B 732 " --> pdb=" O TYR B 666 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL B 668 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 703 " --> pdb=" O GLU B 706 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE B 708 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU B 701 " --> pdb=" O PHE B 708 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE B 710 " --> pdb=" O TYR B 699 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR B 699 " --> pdb=" O PHE B 710 " (cutoff:3.500A) 527 hydrogen bonds defined for protein. 1473 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 1.40 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=" 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=" N VAL B 495 " pdb=" CA VAL B 495 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.17e-02 7.31e+03 7.82e+00 bond pdb=" N CYS B 497 " pdb=" CA CYS B 497 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.23e-02 6.61e+03 7.41e+00 ... (remaining 13407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 17801 2.07 - 4.15: 339 4.15 - 6.22: 40 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=" C LYS A 494 " pdb=" CA LYS A 494 " pdb=" CB LYS A 494 " ideal model delta sigma weight residual 109.75 116.77 -7.02 1.65e+00 3.67e-01 1.81e+01 angle pdb=" N PRO B 468 " pdb=" CA PRO B 468 " pdb=" C PRO B 468 " ideal model delta sigma weight residual 111.32 118.47 -7.15 1.71e+00 3.42e-01 1.75e+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: 1608 0.057 - 0.113: 294 0.113 - 0.170: 57 0.170 - 0.227: 13 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=" 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 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 2.35 -2.62 -0.27 2.00e-01 2.50e+01 1.86e+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: 0.02 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: 2.650 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.760 Find NCS groups from input model: 0.180 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 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= 0.261 Angle : 0.676 10.375 18188 Z= 0.402 Chirality : 0.051 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 0.00513 / 0.26 (13412) covalent geometry : angle 0.67567 / 0.40 (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 : 0.537 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: 0.1355 time to fit residues: 47.7093 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 : 0.549 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A 242 ASN A 454 HIS ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN B 382 ASN ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.105392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.074142 restraints weight = 48145.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.076679 restraints weight = 26669.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.078276 restraints weight = 18879.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.079339 restraints weight = 15461.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.079675 restraints weight = 13645.405| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13412 Z= 0.140 Angle : 0.650 11.229 18188 Z= 0.329 Chirality : 0.045 0.192 1980 Planarity : 0.004 0.055 2268 Dihedral : 9.151 69.882 1884 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.54 % Favored : 96.33 % Rotamer: Outliers : 1.00 % Allowed : 8.24 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.21), residues: 1554 helix: 1.30 (0.24), residues: 464 sheet: -0.08 (0.29), residues: 304 loop : -0.74 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 570 TYR 0.022 0.002 TYR B 9 PHE 0.016 0.001 PHE A 481 TRP 0.013 0.001 TRP B 214 HIS 0.015 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (13412) covalent geometry : angle 0.65029 / 0.33 (18188) hydrogen bonds : bond 0.04442 / 2.81 ( 525) hydrogen bonds : angle 6.28075 / 4.32 ( 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 177 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.515 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 76 MET cc_start: 0.5399 (ppp) cc_final: 0.5182 (ppp) REVERT: A 91 LYS cc_start: 0.9473 (mmtt) cc_final: 0.9249 (mmtt) REVERT: A 206 PHE cc_start: 0.9171 (m-80) cc_final: 0.8910 (m-80) REVERT: A 238 TYR cc_start: 0.8521 (m-80) cc_final: 0.8232 (m-80) REVERT: A 266 MET cc_start: 0.9246 (ptm) cc_final: 0.8528 (ppp) REVERT: A 403 MET cc_start: 0.8259 (tpp) cc_final: 0.7996 (tpt) REVERT: A 493 LEU cc_start: 0.9514 (tp) cc_final: 0.9103 (pp) REVERT: A 630 ILE cc_start: 0.9596 (mm) cc_final: 0.9214 (tp) REVERT: A 729 MET cc_start: 0.8117 (ttm) cc_final: 0.7500 (mtp) REVERT: B 119 GLU cc_start: 0.8436 (tp30) cc_final: 0.8235 (tp30) REVERT: B 275 MET cc_start: 0.7349 (ppp) cc_final: 0.6973 (ppp) REVERT: B 287 MET cc_start: 0.8791 (tpt) cc_final: 0.8575 (tpp) REVERT: B 448 GLU cc_start: 0.9399 (mm-30) cc_final: 0.8869 (tp30) outliers start: 14 outliers final: 9 residues processed: 171 average time/residue: 0.1295 time to fit residues: 31.6583 Evaluate side-chains 132 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 288 LEU 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 673 LYS 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: 1.9990 chunk 119 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 139 optimal weight: 0.1980 chunk 84 optimal weight: 10.0000 chunk 129 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN B 406 ASN B 454 HIS B 482 HIS ** B 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.104884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.073529 restraints weight = 48904.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.076172 restraints weight = 26949.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.077826 restraints weight = 18989.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.078796 restraints weight = 15406.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.079475 restraints weight = 13693.305| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13412 Z= 0.129 Angle : 0.592 12.287 18188 Z= 0.301 Chirality : 0.043 0.167 1980 Planarity : 0.004 0.060 2268 Dihedral : 9.387 65.423 1884 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.70 % Favored : 97.17 % Rotamer: Outliers : 1.43 % Allowed : 10.74 % Favored : 87.82 % 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: 0.19 (0.21), residues: 1554 helix: 1.44 (0.24), residues: 458 sheet: -0.05 (0.28), residues: 338 loop : -0.56 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 455 TYR 0.024 0.001 TYR B 562 PHE 0.024 0.001 PHE B 481 TRP 0.008 0.001 TRP A 549 HIS 0.010 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (13412) covalent geometry : angle 0.59229 / 0.30 (18188) hydrogen bonds : bond 0.03875 / 2.51 ( 525) hydrogen bonds : angle 5.70838 / 3.92 ( 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 156 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8149 (mtm) cc_final: 0.7504 (mtm) REVERT: A 160 LYS cc_start: 0.8935 (tttp) cc_final: 0.8258 (tppt) REVERT: A 172 THR cc_start: 0.9340 (m) cc_final: 0.8925 (p) REVERT: A 175 LEU cc_start: 0.9028 (tt) cc_final: 0.8521 (mp) REVERT: A 238 TYR cc_start: 0.8521 (m-80) cc_final: 0.8251 (m-80) REVERT: A 266 MET cc_start: 0.9145 (ptm) cc_final: 0.8481 (ppp) REVERT: A 275 MET cc_start: 0.6726 (pmm) cc_final: 0.5110 (pmm) REVERT: A 535 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9170 (tt) REVERT: A 729 MET cc_start: 0.8155 (ttm) cc_final: 0.7454 (mtp) REVERT: B 275 MET cc_start: 0.7390 (ppp) cc_final: 0.7027 (ppp) REVERT: B 287 MET cc_start: 0.8787 (tpt) cc_final: 0.8500 (tpp) REVERT: B 448 GLU cc_start: 0.9390 (mm-30) cc_final: 0.8865 (tp30) outliers start: 20 outliers final: 14 residues processed: 145 average time/residue: 0.1164 time to fit residues: 25.1465 Evaluate side-chains 128 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 288 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 58 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 43 optimal weight: 0.0030 chunk 127 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 overall best weight: 1.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 HIS ** 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 = 0.4068 r_free = 0.4068 target = 0.103279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.072230 restraints weight = 49105.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.074617 restraints weight = 27584.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.076217 restraints weight = 19302.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.077248 restraints weight = 15707.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.077823 restraints weight = 13863.153| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13412 Z= 0.150 Angle : 0.572 11.501 18188 Z= 0.292 Chirality : 0.043 0.156 1980 Planarity : 0.004 0.051 2268 Dihedral : 9.918 64.663 1884 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.35 % Favored : 96.53 % Rotamer: Outliers : 1.79 % Allowed : 11.96 % 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: 0.32 (0.21), residues: 1554 helix: 1.52 (0.25), residues: 452 sheet: 0.04 (0.29), residues: 320 loop : -0.44 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 455 TYR 0.023 0.001 TYR B 643 PHE 0.017 0.001 PHE A 716 TRP 0.008 0.001 TRP A 549 HIS 0.005 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (13412) covalent geometry : angle 0.57219 / 0.29 (18188) hydrogen bonds : bond 0.03644 / 2.36 ( 525) hydrogen bonds : angle 5.51746 / 3.78 ( 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: 25 poor density : 120 time to evaluate : 0.507 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: 0.9327 (m) cc_final: 0.8941 (p) REVERT: A 175 LEU cc_start: 0.9033 (tt) cc_final: 0.8524 (mp) REVERT: A 266 MET cc_start: 0.9087 (ptm) cc_final: 0.8354 (ppp) REVERT: A 275 MET cc_start: 0.6861 (pmm) cc_final: 0.5360 (pmm) REVERT: A 451 LYS cc_start: 0.9549 (ptpt) cc_final: 0.9341 (pttp) REVERT: A 535 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9245 (tt) REVERT: A 729 MET cc_start: 0.8257 (ttm) cc_final: 0.7545 (mtp) REVERT: B 189 ILE cc_start: 0.9013 (mm) cc_final: 0.8686 (tp) REVERT: B 275 MET cc_start: 0.7193 (ppp) cc_final: 0.6662 (ppp) REVERT: B 287 MET cc_start: 0.8798 (tpt) cc_final: 0.8477 (tpp) REVERT: B 322 PHE cc_start: 0.9342 (m-80) cc_final: 0.9094 (m-80) REVERT: B 448 GLU cc_start: 0.9411 (mm-30) cc_final: 0.8895 (tp30) outliers start: 25 outliers final: 15 residues processed: 133 average time/residue: 0.1185 time to fit residues: 23.4143 Evaluate side-chains 124 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 535 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 159 TYR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 39 ASN A 242 ASN A 496 GLN A 568 HIS A 726 ASN ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS B 242 ASN B 726 ASN ** B 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.098061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.067813 restraints weight = 50436.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.070114 restraints weight = 27801.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.071594 restraints weight = 19834.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.072411 restraints weight = 16241.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.072996 restraints weight = 14522.280| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 13412 Z= 0.316 Angle : 0.718 12.744 18188 Z= 0.367 Chirality : 0.046 0.193 1980 Planarity : 0.005 0.054 2268 Dihedral : 10.456 62.130 1884 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.18 % Favored : 95.69 % Rotamer: Outliers : 2.87 % Allowed : 13.04 % Favored : 84.10 % 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: 0.07 (0.21), residues: 1554 helix: 1.15 (0.24), residues: 456 sheet: -0.10 (0.30), residues: 308 loop : -0.50 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 455 TYR 0.024 0.002 TYR B 562 PHE 0.018 0.002 PHE B 531 TRP 0.010 0.002 TRP A 131 HIS 0.009 0.002 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.32 (13412) covalent geometry : angle 0.71833 / 0.37 (18188) hydrogen bonds : bond 0.04114 / 2.64 ( 525) hydrogen bonds : angle 5.77933 / 3.93 ( 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 146 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 THR cc_start: 0.9334 (m) cc_final: 0.8988 (p) REVERT: B 275 MET cc_start: 0.7431 (ppp) cc_final: 0.6875 (ppp) REVERT: B 287 MET cc_start: 0.8803 (tpt) cc_final: 0.8346 (tpt) REVERT: B 454 HIS cc_start: 0.8623 (m170) cc_final: 0.8401 (m90) outliers start: 40 outliers final: 27 residues processed: 130 average time/residue: 0.1172 time to fit residues: 22.7966 Evaluate side-chains 124 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 288 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 568 HIS 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 5 ILE Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 115 PHE Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 238 TYR 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 544 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 774 LEU 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: 2.9990 chunk 35 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 242 ASN A 568 HIS A 726 ASN ** B 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.101233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.070267 restraints weight = 49724.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.072694 restraints weight = 27242.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.074258 restraints weight = 19386.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.075213 restraints weight = 15870.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.075765 restraints weight = 14119.911| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13412 Z= 0.127 Angle : 0.623 16.402 18188 Z= 0.308 Chirality : 0.044 0.163 1980 Planarity : 0.004 0.049 2268 Dihedral : 10.111 59.694 1884 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.35 % Favored : 96.53 % Rotamer: Outliers : 1.93 % Allowed : 14.54 % Favored : 83.52 % 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: 0.23 (0.21), residues: 1554 helix: 1.26 (0.24), residues: 458 sheet: -0.08 (0.30), residues: 310 loop : -0.34 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 455 TYR 0.022 0.001 TYR A 238 PHE 0.011 0.001 PHE B 481 TRP 0.009 0.001 TRP B 214 HIS 0.009 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (13412) covalent geometry : angle 0.62282 / 0.31 (18188) hydrogen bonds : bond 0.03598 / 2.33 ( 525) hydrogen bonds : angle 5.42580 / 3.67 ( 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 149 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.506 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: 0.9326 (m) cc_final: 0.8992 (p) REVERT: A 275 MET cc_start: 0.6968 (pmm) cc_final: 0.5250 (pmm) REVERT: A 331 LYS cc_start: 0.8869 (tptt) cc_final: 0.8554 (tptt) REVERT: A 718 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8461 (mt) REVERT: A 729 MET cc_start: 0.8285 (ttm) cc_final: 0.7585 (mtp) REVERT: A 740 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8404 (mpp) REVERT: B 76 MET cc_start: 0.6231 (ppp) cc_final: 0.5931 (ppp) REVERT: B 275 MET cc_start: 0.7333 (ppp) cc_final: 0.6711 (ppp) REVERT: B 287 MET cc_start: 0.8763 (tpt) cc_final: 0.8250 (tpt) REVERT: B 311 PHE cc_start: 0.9182 (m-80) cc_final: 0.8836 (m-80) REVERT: B 322 PHE cc_start: 0.9415 (m-80) cc_final: 0.9099 (m-80) REVERT: B 454 HIS cc_start: 0.8539 (m170) cc_final: 0.8330 (m-70) outliers start: 27 outliers final: 18 residues processed: 135 average time/residue: 0.1111 time to fit residues: 22.5995 Evaluate side-chains 122 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 479 LYS Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 718 ILE 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 111 VAL 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 238 TYR 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 646 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 120 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 131 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 568 HIS A 726 ASN B 210 ASN ** B 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.101225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.070386 restraints weight = 49544.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.072867 restraints weight = 27193.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.074393 restraints weight = 19243.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.075377 restraints weight = 15748.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.075888 restraints weight = 13998.319| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4031 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= 0.134 Angle : 0.632 16.274 18188 Z= 0.312 Chirality : 0.044 0.158 1980 Planarity : 0.004 0.049 2268 Dihedral : 10.166 59.947 1884 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.28 % Favored : 96.59 % Rotamer: Outliers : 1.86 % Allowed : 15.83 % Favored : 82.31 % 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: 0.28 (0.21), residues: 1554 helix: 1.28 (0.24), residues: 458 sheet: -0.02 (0.30), residues: 310 loop : -0.30 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 98 TYR 0.030 0.001 TYR B 243 PHE 0.015 0.001 PHE A 311 TRP 0.008 0.001 TRP B 549 HIS 0.007 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (13412) covalent geometry : angle 0.63249 / 0.31 (18188) hydrogen bonds : bond 0.03598 / 2.34 ( 525) hydrogen bonds : angle 5.34329 / 3.61 ( 1473) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7360 (pmm) cc_final: 0.6962 (pmm) REVERT: A 172 THR cc_start: 0.9299 (m) cc_final: 0.8970 (p) REVERT: A 275 MET cc_start: 0.7002 (pmm) cc_final: 0.5372 (pmm) REVERT: A 331 LYS cc_start: 0.8878 (tptt) cc_final: 0.8576 (tptt) REVERT: A 493 LEU cc_start: 0.9548 (tp) cc_final: 0.9169 (pp) REVERT: A 729 MET cc_start: 0.8336 (ttm) cc_final: 0.7664 (mtp) REVERT: A 740 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8433 (mpp) REVERT: B 275 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6705 (ppp) REVERT: B 287 MET cc_start: 0.8774 (tpt) cc_final: 0.8250 (tpt) REVERT: B 311 PHE cc_start: 0.9227 (m-80) cc_final: 0.8878 (m-80) REVERT: B 322 PHE cc_start: 0.9458 (m-80) cc_final: 0.9155 (m-80) REVERT: B 454 HIS cc_start: 0.8577 (m170) cc_final: 0.8349 (m-70) REVERT: B 729 MET cc_start: 0.7932 (tmm) cc_final: 0.6849 (tmm) outliers start: 26 outliers final: 19 residues processed: 122 average time/residue: 0.1134 time to fit residues: 21.0123 Evaluate side-chains 125 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 479 LYS Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 568 HIS 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 111 VAL Chi-restraints excluded: chain B residue 115 PHE Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 238 TYR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 347 TRP Chi-restraints excluded: chain B residue 479 LYS 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 702 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 12 optimal weight: 0.0070 chunk 36 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 145 optimal weight: 0.9990 chunk 24 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 568 HIS ** B 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.101508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.071026 restraints weight = 49496.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.073530 restraints weight = 26947.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.075079 restraints weight = 18980.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.076028 restraints weight = 15496.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.076619 restraints weight = 13761.792| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13412 Z= 0.128 Angle : 0.627 16.642 18188 Z= 0.306 Chirality : 0.044 0.280 1980 Planarity : 0.004 0.050 2268 Dihedral : 10.221 59.780 1884 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.15 % Favored : 96.72 % Rotamer: Outliers : 1.86 % Allowed : 15.83 % Favored : 82.31 % 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: 0.32 (0.22), residues: 1554 helix: 1.34 (0.24), residues: 458 sheet: -0.03 (0.29), residues: 324 loop : -0.30 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 455 TYR 0.026 0.001 TYR B 243 PHE 0.014 0.001 PHE A 311 TRP 0.008 0.001 TRP B 549 HIS 0.007 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (13412) covalent geometry : angle 0.62724 / 0.31 (18188) hydrogen bonds : bond 0.03514 / 2.28 ( 525) hydrogen bonds : angle 5.24582 / 3.53 ( 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 143 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7311 (pmm) cc_final: 0.6944 (pmm) REVERT: A 172 THR cc_start: 0.9283 (m) cc_final: 0.8960 (p) REVERT: A 183 TYR cc_start: 0.9241 (m-80) cc_final: 0.8829 (m-80) REVERT: A 275 MET cc_start: 0.6938 (pmm) cc_final: 0.5320 (pmm) REVERT: A 740 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8447 (mpp) REVERT: B 275 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6662 (ppp) REVERT: B 287 MET cc_start: 0.8769 (tpt) cc_final: 0.8234 (tpt) REVERT: B 311 PHE cc_start: 0.9230 (m-80) cc_final: 0.8843 (m-80) REVERT: B 322 PHE cc_start: 0.9466 (m-80) cc_final: 0.9096 (m-80) REVERT: B 729 MET cc_start: 0.7939 (tmm) cc_final: 0.6844 (tmm) outliers start: 26 outliers final: 20 residues processed: 130 average time/residue: 0.1146 time to fit residues: 23.0134 Evaluate side-chains 123 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 568 HIS 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 111 VAL Chi-restraints excluded: chain B residue 115 PHE 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 275 MET Chi-restraints excluded: chain B residue 347 TRP Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 540 LEU 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 702 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 32 optimal weight: 0.9980 chunk 103 optimal weight: 0.0970 chunk 136 optimal weight: 0.1980 chunk 49 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 98 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 HIS ** 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 = 0.4058 r_free = 0.4058 target = 0.102353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.071924 restraints weight = 49783.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.074518 restraints weight = 27067.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.076102 restraints weight = 18966.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.077079 restraints weight = 15406.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.077629 restraints weight = 13646.637| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13412 Z= 0.113 Angle : 0.626 17.177 18188 Z= 0.303 Chirality : 0.044 0.228 1980 Planarity : 0.004 0.049 2268 Dihedral : 10.227 59.935 1884 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.35 % Favored : 96.53 % Rotamer: Outliers : 1.72 % Allowed : 16.55 % Favored : 81.73 % 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: 0.36 (0.22), residues: 1554 helix: 1.37 (0.24), residues: 458 sheet: 0.03 (0.30), residues: 324 loop : -0.28 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 433 TYR 0.025 0.001 TYR B 243 PHE 0.016 0.001 PHE B 481 TRP 0.008 0.001 TRP B 549 HIS 0.004 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (13412) covalent geometry : angle 0.62629 / 0.30 (18188) hydrogen bonds : bond 0.03436 / 2.24 ( 525) hydrogen bonds : angle 5.16738 / 3.49 ( 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 130 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7365 (pmm) cc_final: 0.7002 (pmm) REVERT: A 172 THR cc_start: 0.9289 (m) cc_final: 0.8984 (p) REVERT: A 183 TYR cc_start: 0.9220 (m-80) cc_final: 0.8808 (m-80) REVERT: A 275 MET cc_start: 0.6949 (pmm) cc_final: 0.5355 (pmm) REVERT: B 76 MET cc_start: 0.6119 (ppp) cc_final: 0.5877 (ppp) REVERT: B 275 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6697 (ppp) REVERT: B 287 MET cc_start: 0.8755 (tpt) cc_final: 0.8213 (tpt) REVERT: B 311 PHE cc_start: 0.9220 (m-80) cc_final: 0.8782 (m-80) REVERT: B 322 PHE cc_start: 0.9455 (m-80) cc_final: 0.9071 (m-80) REVERT: B 454 HIS cc_start: 0.9205 (m-70) cc_final: 0.8584 (m-70) outliers start: 24 outliers final: 19 residues processed: 120 average time/residue: 0.1069 time to fit residues: 19.6942 Evaluate side-chains 120 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 540 LEU Chi-restraints excluded: chain A residue 568 HIS 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 115 PHE 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 275 MET Chi-restraints excluded: chain B residue 347 TRP Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 8 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 16 optimal weight: 0.0470 chunk 23 optimal weight: 10.0000 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 HIS ** A 746 GLN ** 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 = 0.4008 r_free = 0.4008 target = 0.099234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.068497 restraints weight = 50683.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.070942 restraints weight = 27942.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.072445 restraints weight = 19834.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.073322 restraints weight = 16247.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.073946 restraints weight = 14526.514| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 13412 Z= 0.204 Angle : 0.665 17.067 18188 Z= 0.326 Chirality : 0.045 0.348 1980 Planarity : 0.004 0.049 2268 Dihedral : 10.349 59.988 1884 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.18 % Favored : 95.69 % Rotamer: Outliers : 1.65 % Allowed : 16.69 % Favored : 81.66 % 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: 0.34 (0.22), residues: 1554 helix: 1.39 (0.25), residues: 458 sheet: -0.06 (0.30), residues: 312 loop : -0.27 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 433 TYR 0.025 0.001 TYR B 243 PHE 0.022 0.002 PHE B 481 TRP 0.007 0.001 TRP A 131 HIS 0.011 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (13412) covalent geometry : angle 0.66518 / 0.33 (18188) hydrogen bonds : bond 0.03506 / 2.26 ( 525) hydrogen bonds : angle 5.28498 / 3.57 ( 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 124 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7412 (pmm) cc_final: 0.7048 (pmm) REVERT: A 172 THR cc_start: 0.9307 (m) cc_final: 0.9013 (p) REVERT: A 183 TYR cc_start: 0.9247 (m-80) cc_final: 0.8805 (m-80) REVERT: A 332 LEU cc_start: 0.9678 (tp) cc_final: 0.9382 (mt) REVERT: A 740 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8497 (mpp) REVERT: B 76 MET cc_start: 0.6459 (ppp) cc_final: 0.6232 (ppp) REVERT: B 275 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6744 (ppp) REVERT: B 287 MET cc_start: 0.8757 (tpt) cc_final: 0.8300 (tpt) REVERT: B 454 HIS cc_start: 0.9221 (m-70) cc_final: 0.8653 (m-70) REVERT: B 729 MET cc_start: 0.8122 (tmm) cc_final: 0.7012 (tmm) outliers start: 23 outliers final: 18 residues processed: 113 average time/residue: 0.1070 time to fit residues: 18.4121 Evaluate side-chains 119 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 540 LEU Chi-restraints excluded: chain A residue 568 HIS 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 115 PHE 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 275 MET Chi-restraints excluded: chain B residue 347 TRP Chi-restraints excluded: chain B residue 479 LYS 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 702 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 54 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 HIS ** A 746 GLN ** 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 = 0.4014 r_free = 0.4014 target = 0.099498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.069127 restraints weight = 50211.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.071504 restraints weight = 27350.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.073002 restraints weight = 19382.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.073913 restraints weight = 15852.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.074478 restraints weight = 14114.581| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13412 Z= 0.176 Angle : 0.666 16.747 18188 Z= 0.321 Chirality : 0.045 0.374 1980 Planarity : 0.004 0.072 2268 Dihedral : 10.322 59.596 1884 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.93 % Favored : 95.95 % Rotamer: Outliers : 1.65 % Allowed : 16.83 % Favored : 81.52 % 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: 0.32 (0.22), residues: 1554 helix: 1.38 (0.24), residues: 458 sheet: -0.08 (0.31), residues: 298 loop : -0.29 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 98 TYR 0.025 0.001 TYR B 243 PHE 0.020 0.001 PHE B 481 TRP 0.010 0.001 TRP B 214 HIS 0.007 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (13412) covalent geometry : angle 0.66583 / 0.32 (18188) hydrogen bonds : bond 0.03467 / 2.23 ( 525) hydrogen bonds : angle 5.24939 / 3.55 ( 1473) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2939.88 seconds wall clock time: 51 minutes 28.31 seconds (3088.31 seconds total)