Starting phenix.real_space_refine on Fri Jan 17 20:32:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xjs_38404/01_2025/8xjs_38404.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xjs_38404/01_2025/8xjs_38404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xjs_38404/01_2025/8xjs_38404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xjs_38404/01_2025/8xjs_38404.map" model { file = "/net/cci-nas-00/data/ceres_data/8xjs_38404/01_2025/8xjs_38404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xjs_38404/01_2025/8xjs_38404.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 76 5.16 5 C 7106 2.51 5 N 1920 2.21 5 O 2076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11178 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 69 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "B" Number of atoms: 4193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4193 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 25, 'TRANS': 491} Chain breaks: 5 Chain: "A" Number of atoms: 6302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6302 Classifications: {'peptide': 781} Link IDs: {'PTRANS': 42, 'TRANS': 738} Chain breaks: 3 Chain: "C" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 359 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain breaks: 1 Chain: "E" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain breaks: 1 Time building chain proxies: 8.79, per 1000 atoms: 0.79 Number of scatterers: 11178 At special positions: 0 Unit cell: (106.26, 130.68, 177.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 76 16.00 O 2076 8.00 N 1920 7.00 C 7106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 674 " - pdb=" SG CYS B 887 " distance=2.03 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 822 " distance=2.03 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 53 " distance=2.03 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 209 " distance=2.04 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 215 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 228 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 235 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 252 " distance=2.03 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 264 " distance=2.03 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 280 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 311 " distance=2.04 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 328 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 462 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 674 " - pdb=" SG CYS A 887 " distance=2.03 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 822 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 48 " distance=2.03 Simple disulfide: pdb=" SG CYS C 18 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 52 " distance=2.03 Simple disulfide: pdb=" SG CYS E 18 " - pdb=" SG CYS E 61 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.4 seconds 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2604 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 27 sheets defined 16.6% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'D' and resid 10 through 18 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.600A pdb=" N ALA B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 376 through 386 Processing helix chain 'B' and resid 462 through 472 removed outlier: 3.830A pdb=" N ILE B 466 " --> pdb=" O CYS B 462 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 568 through 573 removed outlier: 4.074A pdb=" N SER B 572 " --> pdb=" O ASN B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 741 Processing helix chain 'B' and resid 835 through 840 removed outlier: 4.003A pdb=" N ASP B 839 " --> pdb=" O GLU B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 897 Processing helix chain 'A' and resid 44 through 51 removed outlier: 3.595A pdb=" N LEU A 50 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.624A pdb=" N PHE A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 166 through 170 removed outlier: 3.842A pdb=" N ASP A 169 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 295 Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 377 through 386 Processing helix chain 'A' and resid 405 through 409 removed outlier: 4.430A pdb=" N PHE A 408 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 474 removed outlier: 3.503A pdb=" N ILE A 466 " --> pdb=" O CYS A 462 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 474 " --> pdb=" O GLU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 569 through 573 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 835 through 840 removed outlier: 3.616A pdb=" N ASP A 839 " --> pdb=" O ALA A 836 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP A 840 " --> pdb=" O LYS A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 897 Processing helix chain 'C' and resid 7 through 19 removed outlier: 3.663A pdb=" N VAL C 11 " --> pdb=" O GLY C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 53 through 59 removed outlier: 4.114A pdb=" N MET C 59 " --> pdb=" O ARG C 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 18 Processing helix chain 'E' and resid 54 through 59 Processing sheet with id=AA1, first strand: chain 'B' and resid 340 through 348 removed outlier: 5.999A pdb=" N HIS B 340 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASN B 364 " --> pdb=" O HIS B 340 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 342 " --> pdb=" O ASN B 364 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N SER B 366 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY B 344 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE B 368 " --> pdb=" O GLY B 344 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LYS B 346 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE B 363 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 340 through 348 removed outlier: 5.999A pdb=" N HIS B 340 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASN B 364 " --> pdb=" O HIS B 340 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 342 " --> pdb=" O ASN B 364 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N SER B 366 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY B 344 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE B 368 " --> pdb=" O GLY B 344 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LYS B 346 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N LYS B 396 " --> pdb=" O GLY B 365 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU B 367 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ARG B 398 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ILE B 369 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LYS B 452 " --> pdb=" O TYR B 425 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 498 through 500 removed outlier: 5.946A pdb=" N GLU B 498 " --> pdb=" O LYS B 609 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 502 through 507 Processing sheet with id=AA5, first strand: chain 'B' and resid 557 through 561 removed outlier: 3.620A pdb=" N GLY B 529 " --> pdb=" O LEU B 596 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 626 through 634 removed outlier: 6.455A pdb=" N LYS B 641 " --> pdb=" O PRO B 628 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER B 630 " --> pdb=" O ILE B 639 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE B 639 " --> pdb=" O SER B 630 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N SER B 632 " --> pdb=" O GLN B 637 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLN B 637 " --> pdb=" O SER B 632 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 786 through 789 Processing sheet with id=AA8, first strand: chain 'B' and resid 846 through 850 removed outlier: 3.894A pdb=" N VAL B 854 " --> pdb=" O PHE B 850 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 883 through 889 Processing sheet with id=AB1, first strand: chain 'A' and resid 33 through 35 removed outlier: 7.024A pdb=" N GLU A 33 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE A 56 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N CYS A 35 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET A 83 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.375A pdb=" N MET A 38 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEU A 63 " --> pdb=" O MET A 38 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE A 40 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET A 65 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 93 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU A 88 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N PHE A 123 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU A 90 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 120 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLU A 147 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE A 122 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL A 144 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL A 173 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE A 146 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 199 through 201 Processing sheet with id=AB4, first strand: chain 'A' and resid 239 through 243 removed outlier: 3.706A pdb=" N ALA A 254 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASN A 242 " --> pdb=" O CYS A 252 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N CYS A 252 " --> pdb=" O ASN A 242 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AB6, first strand: chain 'A' and resid 273 through 275 Processing sheet with id=AB7, first strand: chain 'A' and resid 305 through 307 Processing sheet with id=AB8, first strand: chain 'A' and resid 319 through 321 Processing sheet with id=AB9, first strand: chain 'A' and resid 338 through 348 removed outlier: 10.649A pdb=" N VAL A 362 " --> pdb=" O HIS A 340 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N LEU A 342 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 9.786A pdb=" N ASN A 364 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY A 344 " --> pdb=" O ASN A 364 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 338 through 348 removed outlier: 10.649A pdb=" N VAL A 362 " --> pdb=" O HIS A 340 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N LEU A 342 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 9.786A pdb=" N ASN A 364 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY A 344 " --> pdb=" O ASN A 364 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE A 454 " --> pdb=" O SER A 426 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR A 428 " --> pdb=" O PHE A 454 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 498 through 500 removed outlier: 5.799A pdb=" N GLU A 498 " --> pdb=" O LYS A 609 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 502 through 507 Processing sheet with id=AC4, first strand: chain 'A' and resid 557 through 561 removed outlier: 3.796A pdb=" N TYR A 534 " --> pdb=" O THR A 557 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 529 " --> pdb=" O LEU A 596 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 626 through 631 removed outlier: 6.805A pdb=" N LYS A 641 " --> pdb=" O PRO A 628 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 630 " --> pdb=" O ILE A 639 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 639 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 786 through 789 removed outlier: 3.531A pdb=" N ALA A 826 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 846 through 849 Processing sheet with id=AC8, first strand: chain 'A' and resid 883 through 889 removed outlier: 6.430A pdb=" N ILE A 913 " --> pdb=" O TRP A 924 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N TRP A 924 " --> pdb=" O ILE A 913 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ALA A 915 " --> pdb=" O GLY A 922 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 883 through 889 326 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.19 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3657 1.34 - 1.46: 2637 1.46 - 1.58: 5055 1.58 - 1.70: 0 1.70 - 1.82: 94 Bond restraints: 11443 Sorted by residual: bond pdb=" N SER B 823 " pdb=" CA SER B 823 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.87e+00 bond pdb=" CA PRO A 563 " pdb=" C PRO A 563 " ideal model delta sigma weight residual 1.514 1.526 -0.012 5.50e-03 3.31e+04 4.89e+00 bond pdb=" CA PHE B 454 " pdb=" CB PHE B 454 " ideal model delta sigma weight residual 1.522 1.547 -0.025 1.27e-02 6.20e+03 3.86e+00 bond pdb=" CA ASN A 42 " pdb=" C ASN A 42 " ideal model delta sigma weight residual 1.523 1.499 0.024 1.34e-02 5.57e+03 3.31e+00 bond pdb=" CA TYR A 94 " pdb=" C TYR A 94 " ideal model delta sigma weight residual 1.525 1.502 0.023 1.28e-02 6.10e+03 3.22e+00 ... (remaining 11438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 15090 1.96 - 3.92: 344 3.92 - 5.88: 55 5.88 - 7.84: 5 7.84 - 9.80: 6 Bond angle restraints: 15500 Sorted by residual: angle pdb=" N SER B 823 " pdb=" CA SER B 823 " pdb=" C SER B 823 " ideal model delta sigma weight residual 110.80 119.30 -8.50 2.13e+00 2.20e-01 1.59e+01 angle pdb=" C GLN B 811 " pdb=" CA GLN B 811 " pdb=" CB GLN B 811 " ideal model delta sigma weight residual 110.34 115.61 -5.27 1.40e+00 5.10e-01 1.42e+01 angle pdb=" N ASN A 42 " pdb=" CA ASN A 42 " pdb=" C ASN A 42 " ideal model delta sigma weight residual 110.80 118.22 -7.42 2.13e+00 2.20e-01 1.21e+01 angle pdb=" N MET E 59 " pdb=" CA MET E 59 " pdb=" C MET E 59 " ideal model delta sigma weight residual 112.97 109.39 3.58 1.06e+00 8.90e-01 1.14e+01 angle pdb=" CB MET B 858 " pdb=" CG MET B 858 " pdb=" SD MET B 858 " ideal model delta sigma weight residual 112.70 122.50 -9.80 3.00e+00 1.11e-01 1.07e+01 ... (remaining 15495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6050 17.99 - 35.97: 655 35.97 - 53.96: 171 53.96 - 71.94: 23 71.94 - 89.93: 14 Dihedral angle restraints: 6913 sinusoidal: 2876 harmonic: 4037 Sorted by residual: dihedral pdb=" CB CYS A 255 " pdb=" SG CYS A 255 " pdb=" SG CYS A 264 " pdb=" CB CYS A 264 " ideal model delta sinusoidal sigma weight residual -86.00 -168.62 82.62 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS A 35 " pdb=" SG CYS A 35 " pdb=" SG CYS A 53 " pdb=" CB CYS A 53 " ideal model delta sinusoidal sigma weight residual 93.00 154.34 -61.34 1 1.00e+01 1.00e-02 5.00e+01 dihedral pdb=" CB CYS B 813 " pdb=" SG CYS B 813 " pdb=" SG CYS B 822 " pdb=" CB CYS B 822 " ideal model delta sinusoidal sigma weight residual -86.00 -31.16 -54.84 1 1.00e+01 1.00e-02 4.07e+01 ... (remaining 6910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1265 0.049 - 0.099: 307 0.099 - 0.148: 97 0.148 - 0.197: 7 0.197 - 0.246: 1 Chirality restraints: 1677 Sorted by residual: chirality pdb=" CB THR B 598 " pdb=" CA THR B 598 " pdb=" OG1 THR B 598 " pdb=" CG2 THR B 598 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ASN B 791 " pdb=" N ASN B 791 " pdb=" C ASN B 791 " pdb=" CB ASN B 791 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.63e-01 chirality pdb=" CA SER B 823 " pdb=" N SER B 823 " pdb=" C SER B 823 " pdb=" CB SER B 823 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.37e-01 ... (remaining 1674 not shown) Planarity restraints: 2002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 441 " -0.021 2.00e-02 2.50e+03 1.65e-02 6.83e+00 pdb=" CG TRP B 441 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP B 441 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 441 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 441 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 441 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP B 441 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 441 " 0.015 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 441 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 441 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 659 " -0.016 2.00e-02 2.50e+03 1.52e-02 5.76e+00 pdb=" CG TRP B 659 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 659 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP B 659 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 659 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 659 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 659 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 659 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 659 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 659 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 312 " -0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO A 313 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 313 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 313 " -0.029 5.00e-02 4.00e+02 ... (remaining 1999 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1494 2.75 - 3.29: 10708 3.29 - 3.83: 18442 3.83 - 4.36: 21688 4.36 - 4.90: 37126 Nonbonded interactions: 89458 Sorted by model distance: nonbonded pdb=" NZ LYS A 346 " pdb=" OE1 GLU A 356 " model vdw 2.216 3.120 nonbonded pdb=" O LEU B 463 " pdb=" ND1 HIS B 467 " model vdw 2.216 3.120 nonbonded pdb=" NE ARG A 92 " pdb=" OE1 GLU A 124 " model vdw 2.225 3.120 nonbonded pdb=" OG SER B 567 " pdb=" OG SER B 572 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR A 157 " pdb=" O CYS A 209 " model vdw 2.248 3.040 ... (remaining 89453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 8.540 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: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.540 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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 0.050 11443 Z= 0.323 Angle : 0.711 9.799 15500 Z= 0.387 Chirality : 0.047 0.246 1677 Planarity : 0.004 0.053 2002 Dihedral : 15.751 89.930 4237 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.24 % Favored : 94.61 % Rotamer: Outliers : 1.29 % Allowed : 19.36 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.23), residues: 1355 helix: 0.04 (0.42), residues: 160 sheet: 0.18 (0.30), residues: 326 loop : -0.63 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 659 HIS 0.009 0.001 HIS B 456 PHE 0.026 0.002 PHE E 16 TYR 0.025 0.001 TYR B 655 ARG 0.013 0.001 ARG A 807 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8037 (t0) REVERT: A 858 MET cc_start: 0.4462 (tpt) cc_final: 0.3270 (mmm) REVERT: E 20 ASP cc_start: 0.8272 (p0) cc_final: 0.8065 (p0) REVERT: E 24 TYR cc_start: 0.6620 (m-80) cc_final: 0.5798 (m-10) outliers start: 16 outliers final: 3 residues processed: 106 average time/residue: 0.2918 time to fit residues: 42.7601 Evaluate side-chains 70 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 659 TRP Chi-restraints excluded: chain B residue 821 ARG Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 20.0000 chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 107 optimal weight: 0.4980 chunk 41 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 124 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 885 HIS A 48 HIS A 61 GLN ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 HIS ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.116562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.071796 restraints weight = 37440.896| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 6.48 r_work: 0.3065 rms_B_bonded: 5.79 restraints_weight: 2.0000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11443 Z= 0.193 Angle : 0.605 10.250 15500 Z= 0.320 Chirality : 0.045 0.165 1677 Planarity : 0.004 0.052 2002 Dihedral : 4.905 40.352 1526 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.09 % Favored : 94.83 % Rotamer: Outliers : 1.93 % Allowed : 17.99 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.23), residues: 1355 helix: 0.45 (0.44), residues: 160 sheet: 0.18 (0.29), residues: 330 loop : -0.56 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 556 HIS 0.004 0.001 HIS A 274 PHE 0.016 0.001 PHE B 592 TYR 0.032 0.001 TYR E 60 ARG 0.006 0.000 ARG B 729 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 399 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8124 (tpm170) REVERT: B 446 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8090 (tp) REVERT: A 560 ASP cc_start: 0.9105 (m-30) cc_final: 0.8117 (t0) REVERT: A 858 MET cc_start: 0.3954 (tpt) cc_final: 0.3192 (mmm) REVERT: C 59 MET cc_start: 0.9044 (mtm) cc_final: 0.8821 (mtm) outliers start: 24 outliers final: 7 residues processed: 98 average time/residue: 0.2257 time to fit residues: 33.0423 Evaluate side-chains 73 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 399 ARG Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain E residue 23 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 136 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 113 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 103 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 64 optimal weight: 0.1980 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 48 HIS A 303 GLN ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS A 437 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.116625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.072263 restraints weight = 37797.410| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 6.10 r_work: 0.3066 rms_B_bonded: 5.45 restraints_weight: 2.0000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11443 Z= 0.189 Angle : 0.564 10.656 15500 Z= 0.298 Chirality : 0.045 0.156 1677 Planarity : 0.004 0.040 2002 Dihedral : 4.557 24.109 1518 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.28 % Favored : 95.65 % Rotamer: Outliers : 1.93 % Allowed : 17.91 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.23), residues: 1355 helix: 0.34 (0.43), residues: 164 sheet: 0.11 (0.29), residues: 330 loop : -0.49 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 441 HIS 0.005 0.001 HIS B 467 PHE 0.016 0.001 PHE B 786 TYR 0.026 0.001 TYR E 60 ARG 0.007 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 399 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8103 (tpm170) REVERT: A 560 ASP cc_start: 0.9112 (m-30) cc_final: 0.8111 (t0) REVERT: A 858 MET cc_start: 0.4014 (tpt) cc_final: 0.3163 (mmm) outliers start: 24 outliers final: 12 residues processed: 89 average time/residue: 0.2189 time to fit residues: 30.0964 Evaluate side-chains 75 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 399 ARG Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain E residue 23 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 114 optimal weight: 30.0000 chunk 78 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 121 optimal weight: 30.0000 chunk 113 optimal weight: 20.0000 chunk 35 optimal weight: 0.0030 chunk 106 optimal weight: 3.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 847 HIS C 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.115500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.070736 restraints weight = 37569.629| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 6.42 r_work: 0.3037 rms_B_bonded: 5.77 restraints_weight: 2.0000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11443 Z= 0.244 Angle : 0.556 8.257 15500 Z= 0.292 Chirality : 0.044 0.147 1677 Planarity : 0.004 0.037 2002 Dihedral : 4.516 21.450 1517 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.58 % Favored : 95.35 % Rotamer: Outliers : 1.93 % Allowed : 17.99 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.23), residues: 1355 helix: 0.14 (0.42), residues: 171 sheet: 0.09 (0.29), residues: 332 loop : -0.54 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 441 HIS 0.004 0.001 HIS A 274 PHE 0.015 0.001 PHE B 592 TYR 0.034 0.001 TYR E 60 ARG 0.004 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 387 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8271 (pp) REVERT: B 399 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8073 (tpm170) REVERT: A 560 ASP cc_start: 0.9130 (m-30) cc_final: 0.8133 (t0) REVERT: A 858 MET cc_start: 0.3962 (tpt) cc_final: 0.3237 (mmm) REVERT: C 59 MET cc_start: 0.9120 (mtp) cc_final: 0.8832 (mtm) outliers start: 24 outliers final: 14 residues processed: 83 average time/residue: 0.2239 time to fit residues: 28.2563 Evaluate side-chains 76 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 399 ARG Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 599 PHE Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain E residue 23 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 102 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 90 optimal weight: 0.4980 chunk 85 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 132 optimal weight: 0.5980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 GLN ** A 325 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 = 0.4238 r_free = 0.4238 target = 0.115337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.069362 restraints weight = 37845.556| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 6.81 r_work: 0.3033 rms_B_bonded: 5.95 restraints_weight: 2.0000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11443 Z= 0.247 Angle : 0.543 8.085 15500 Z= 0.286 Chirality : 0.045 0.189 1677 Planarity : 0.003 0.034 2002 Dihedral : 4.500 21.043 1517 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.72 % Favored : 95.20 % Rotamer: Outliers : 2.65 % Allowed : 17.35 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.23), residues: 1355 helix: 0.12 (0.41), residues: 172 sheet: 0.06 (0.29), residues: 338 loop : -0.52 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP B 441 HIS 0.006 0.001 HIS B 467 PHE 0.014 0.001 PHE B 592 TYR 0.031 0.001 TYR E 60 ARG 0.005 0.000 ARG E 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 61 time to evaluate : 1.264 Fit side-chains revert: symmetry clash REVERT: B 387 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8224 (pp) REVERT: A 65 MET cc_start: 0.9358 (mtt) cc_final: 0.9147 (mtp) REVERT: A 478 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.4430 (ptt180) REVERT: A 560 ASP cc_start: 0.9133 (m-30) cc_final: 0.8111 (t0) REVERT: A 858 MET cc_start: 0.3963 (tpt) cc_final: 0.3316 (mmm) REVERT: C 55 ARG cc_start: 0.8952 (tpt90) cc_final: 0.8689 (tpt90) REVERT: C 59 MET cc_start: 0.9162 (mtp) cc_final: 0.8712 (mtm) outliers start: 33 outliers final: 19 residues processed: 87 average time/residue: 0.2349 time to fit residues: 31.1497 Evaluate side-chains 80 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 399 ARG Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 599 PHE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain E residue 23 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 84 optimal weight: 0.7980 chunk 121 optimal weight: 0.1980 chunk 131 optimal weight: 0.6980 chunk 128 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 112 optimal weight: 20.0000 chunk 127 optimal weight: 30.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 42 ASN ** A 325 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 = 0.4244 r_free = 0.4244 target = 0.116039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.069907 restraints weight = 38214.681| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 6.24 r_work: 0.3052 rms_B_bonded: 5.66 restraints_weight: 2.0000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11443 Z= 0.166 Angle : 0.527 8.311 15500 Z= 0.276 Chirality : 0.044 0.181 1677 Planarity : 0.003 0.033 2002 Dihedral : 4.406 20.210 1517 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.35 % Favored : 95.57 % Rotamer: Outliers : 2.17 % Allowed : 17.75 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.23), residues: 1355 helix: 0.28 (0.43), residues: 164 sheet: 0.07 (0.28), residues: 357 loop : -0.39 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 441 HIS 0.003 0.001 HIS A 456 PHE 0.014 0.001 PHE B 599 TYR 0.030 0.001 TYR E 60 ARG 0.008 0.000 ARG B 821 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 1.286 Fit side-chains revert: symmetry clash REVERT: B 399 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7994 (tpm170) REVERT: B 433 GLN cc_start: 0.8556 (mm110) cc_final: 0.8250 (mm110) REVERT: B 469 MET cc_start: 0.7394 (tpp) cc_final: 0.6985 (tpp) REVERT: A 65 MET cc_start: 0.9315 (mtt) cc_final: 0.9087 (mtp) REVERT: A 560 ASP cc_start: 0.9144 (m-30) cc_final: 0.8086 (t0) REVERT: A 858 MET cc_start: 0.3977 (tpt) cc_final: 0.3195 (mmm) outliers start: 27 outliers final: 20 residues processed: 81 average time/residue: 0.2279 time to fit residues: 29.5289 Evaluate side-chains 79 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 399 ARG Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 599 PHE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain E residue 23 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 50.0000 chunk 60 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 96 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 432 ASN B 458 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.114543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.068219 restraints weight = 38398.046| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 6.29 r_work: 0.3018 rms_B_bonded: 5.68 restraints_weight: 2.0000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11443 Z= 0.301 Angle : 0.566 7.782 15500 Z= 0.296 Chirality : 0.045 0.186 1677 Planarity : 0.003 0.033 2002 Dihedral : 4.545 20.588 1517 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.80 % Favored : 95.06 % Rotamer: Outliers : 2.33 % Allowed : 17.91 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.23), residues: 1355 helix: 0.23 (0.42), residues: 165 sheet: 0.07 (0.29), residues: 338 loop : -0.47 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 441 HIS 0.004 0.001 HIS B 456 PHE 0.014 0.002 PHE B 592 TYR 0.032 0.001 TYR E 60 ARG 0.003 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 387 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8180 (pp) REVERT: A 65 MET cc_start: 0.9342 (mtt) cc_final: 0.9137 (mtp) REVERT: A 478 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.4532 (ptt180) REVERT: C 55 ARG cc_start: 0.8921 (tpt90) cc_final: 0.8681 (tpt90) outliers start: 29 outliers final: 23 residues processed: 83 average time/residue: 0.2296 time to fit residues: 29.4877 Evaluate side-chains 82 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 57 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 399 ARG Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 599 PHE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain E residue 23 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 4 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 100 optimal weight: 0.0170 chunk 80 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.115055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.070138 restraints weight = 37810.460| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 6.57 r_work: 0.3038 rms_B_bonded: 5.84 restraints_weight: 2.0000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11443 Z= 0.188 Angle : 0.535 8.202 15500 Z= 0.279 Chirality : 0.044 0.190 1677 Planarity : 0.003 0.033 2002 Dihedral : 4.440 21.082 1517 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.21 % Favored : 95.72 % Rotamer: Outliers : 2.33 % Allowed : 18.07 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.23), residues: 1355 helix: 0.35 (0.42), residues: 165 sheet: 0.08 (0.28), residues: 352 loop : -0.42 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 441 HIS 0.004 0.001 HIS B 467 PHE 0.015 0.001 PHE B 599 TYR 0.030 0.001 TYR E 60 ARG 0.004 0.000 ARG B 821 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 399 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8013 (tpm170) REVERT: B 433 GLN cc_start: 0.8575 (mm110) cc_final: 0.8368 (mm110) REVERT: B 469 MET cc_start: 0.7754 (tpp) cc_final: 0.7073 (tpp) REVERT: A 65 MET cc_start: 0.9320 (mtt) cc_final: 0.9099 (mtp) REVERT: A 478 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.4393 (ptt180) REVERT: C 55 ARG cc_start: 0.8947 (tpt90) cc_final: 0.8711 (tpt90) REVERT: C 59 MET cc_start: 0.9078 (mtm) cc_final: 0.8680 (mtm) outliers start: 29 outliers final: 22 residues processed: 82 average time/residue: 0.2257 time to fit residues: 28.5523 Evaluate side-chains 83 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 399 ARG Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 599 PHE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain E residue 23 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 45 optimal weight: 40.0000 chunk 134 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 75 optimal weight: 0.0770 chunk 105 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 118 optimal weight: 0.2980 chunk 50 optimal weight: 5.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 432 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.116033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.070509 restraints weight = 37711.006| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 6.59 r_work: 0.3067 rms_B_bonded: 5.84 restraints_weight: 2.0000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11443 Z= 0.150 Angle : 0.517 8.147 15500 Z= 0.271 Chirality : 0.044 0.168 1677 Planarity : 0.003 0.033 2002 Dihedral : 4.235 21.267 1517 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.43 % Favored : 95.50 % Rotamer: Outliers : 1.69 % Allowed : 18.96 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.23), residues: 1355 helix: 0.38 (0.44), residues: 164 sheet: 0.29 (0.29), residues: 340 loop : -0.36 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 441 HIS 0.003 0.000 HIS A 274 PHE 0.013 0.001 PHE D 16 TYR 0.029 0.001 TYR E 60 ARG 0.003 0.000 ARG B 821 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.9270 (mtt) cc_final: 0.9007 (mtp) REVERT: A 478 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.5985 (ptp-170) REVERT: A 531 MET cc_start: 0.8632 (mtt) cc_final: 0.8284 (mpp) REVERT: C 55 ARG cc_start: 0.8950 (tpt90) cc_final: 0.8710 (tpt90) REVERT: C 59 MET cc_start: 0.9081 (mtm) cc_final: 0.8723 (mtm) outliers start: 21 outliers final: 16 residues processed: 78 average time/residue: 0.2195 time to fit residues: 26.4796 Evaluate side-chains 77 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 599 PHE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain E residue 23 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 117 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 127 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.114283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.074001 restraints weight = 37891.947| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 4.82 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11443 Z= 0.373 Angle : 0.598 13.032 15500 Z= 0.310 Chirality : 0.046 0.212 1677 Planarity : 0.004 0.033 2002 Dihedral : 4.533 21.883 1517 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.24 % Favored : 94.69 % Rotamer: Outliers : 1.85 % Allowed : 18.96 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.23), residues: 1355 helix: 0.30 (0.42), residues: 163 sheet: 0.21 (0.29), residues: 343 loop : -0.39 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.001 TRP B 441 HIS 0.005 0.001 HIS B 467 PHE 0.014 0.002 PHE B 599 TYR 0.031 0.001 TYR E 60 ARG 0.004 0.000 ARG E 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 387 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8030 (pp) REVERT: A 478 ARG cc_start: 0.6341 (OUTLIER) cc_final: 0.5955 (ptp-170) REVERT: C 59 MET cc_start: 0.8726 (mtm) cc_final: 0.8415 (mtm) outliers start: 23 outliers final: 21 residues processed: 75 average time/residue: 0.2122 time to fit residues: 25.6946 Evaluate side-chains 80 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 599 PHE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain E residue 23 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 53 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 79 optimal weight: 0.0170 chunk 56 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 113 optimal weight: 20.0000 chunk 128 optimal weight: 40.0000 chunk 35 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.115375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.070481 restraints weight = 38079.709| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 6.64 r_work: 0.3055 rms_B_bonded: 5.90 restraints_weight: 2.0000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11443 Z= 0.165 Angle : 0.537 11.448 15500 Z= 0.279 Chirality : 0.044 0.173 1677 Planarity : 0.003 0.033 2002 Dihedral : 4.330 21.779 1517 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.21 % Favored : 95.72 % Rotamer: Outliers : 1.77 % Allowed : 19.04 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.23), residues: 1355 helix: 0.32 (0.43), residues: 164 sheet: 0.29 (0.28), residues: 353 loop : -0.34 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 441 HIS 0.003 0.001 HIS A 236 PHE 0.011 0.001 PHE B 592 TYR 0.031 0.001 TYR E 60 ARG 0.003 0.000 ARG B 821 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10648.50 seconds wall clock time: 192 minutes 59.59 seconds (11579.59 seconds total)