Starting phenix.real_space_refine on Wed Sep 17 20:51:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xjs_38404/09_2025/8xjs_38404.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xjs_38404/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xjs_38404/09_2025/8xjs_38404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xjs_38404/09_2025/8xjs_38404.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xjs_38404/09_2025/8xjs_38404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xjs_38404/09_2025/8xjs_38404.map" } resolution = 3.24 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= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.09, per 1000 atoms: 0.28 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: 0.92 Conformation dependent library (CDL) restraints added in 636.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.40 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: 2.37 Time building geometry restraints manager: 1.27 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: 13.540 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: 0.370 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.420 Find NCS groups from input model: 0.060 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.030 ------------------------------------------------------------------------------- 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 11467 Z= 0.231 Angle : 0.712 9.799 15548 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.013 0.001 ARG A 807 TYR 0.025 0.001 TYR B 655 PHE 0.026 0.002 PHE E 16 TRP 0.040 0.002 TRP B 659 HIS 0.009 0.001 HIS B 456 Details of bonding type rmsd covalent geometry : bond 0.00497 (11443) covalent geometry : angle 0.71055 (15500) SS BOND : bond 0.00272 ( 24) SS BOND : angle 1.12647 ( 48) hydrogen bonds : bond 0.21517 ( 308) hydrogen bonds : angle 8.58350 ( 852) *********************** 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 : 0.471 Fit side-chains 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: 0.1226 time to fit residues: 17.9112 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 : 0.465 ------------------------------------------------------------------------------- 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 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0770 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.0050 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.4552 ------------------------------------------------------------------------------- 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** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 42 ASN 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 = 0.4259 r_free = 0.4259 target = 0.116957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.072286 restraints weight = 37827.668| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 5.88 r_work: 0.3082 rms_B_bonded: 5.43 restraints_weight: 2.0000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11467 Z= 0.123 Angle : 0.603 9.331 15548 Z= 0.320 Chirality : 0.045 0.169 1677 Planarity : 0.004 0.051 2002 Dihedral : 4.865 39.038 1526 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.09 % Favored : 94.83 % Rotamer: Outliers : 1.93 % Allowed : 17.51 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.23), residues: 1355 helix: 0.38 (0.44), residues: 161 sheet: 0.17 (0.29), residues: 334 loop : -0.53 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 729 TYR 0.030 0.001 TYR E 60 PHE 0.015 0.001 PHE B 592 TRP 0.024 0.001 TRP A 556 HIS 0.004 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00262 (11443) covalent geometry : angle 0.60152 (15500) SS BOND : bond 0.00767 ( 24) SS BOND : angle 1.04232 ( 48) hydrogen bonds : bond 0.04513 ( 308) hydrogen bonds : angle 6.61760 ( 852) *********************** 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 102 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 446 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8098 (tp) REVERT: A 560 ASP cc_start: 0.9093 (m-30) cc_final: 0.8106 (t0) REVERT: A 858 MET cc_start: 0.3993 (tpt) cc_final: 0.3102 (mmm) outliers start: 24 outliers final: 7 residues processed: 100 average time/residue: 0.1010 time to fit residues: 15.2068 Evaluate side-chains 74 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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** B 885 HIS A 48 HIS ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS A 437 GLN C 15 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.116002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.071550 restraints weight = 37943.766| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 6.45 r_work: 0.3049 rms_B_bonded: 5.81 restraints_weight: 2.0000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11467 Z= 0.156 Angle : 0.586 10.997 15548 Z= 0.308 Chirality : 0.045 0.184 1677 Planarity : 0.004 0.041 2002 Dihedral : 4.603 23.103 1518 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.43 % Favored : 95.50 % Rotamer: Outliers : 2.09 % Allowed : 17.67 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.23), residues: 1355 helix: 0.06 (0.42), residues: 170 sheet: 0.10 (0.29), residues: 330 loop : -0.55 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 74 TYR 0.029 0.001 TYR E 60 PHE 0.016 0.001 PHE B 592 TRP 0.037 0.001 TRP B 441 HIS 0.004 0.001 HIS B 467 Details of bonding type rmsd covalent geometry : bond 0.00366 (11443) covalent geometry : angle 0.58006 (15500) SS BOND : bond 0.00404 ( 24) SS BOND : angle 1.57399 ( 48) hydrogen bonds : bond 0.04011 ( 308) hydrogen bonds : angle 6.23543 ( 852) *********************** 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 93 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: B 399 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8087 (tpm170) REVERT: A 560 ASP cc_start: 0.9122 (m-30) cc_final: 0.8139 (t0) REVERT: A 858 MET cc_start: 0.3972 (tpt) cc_final: 0.3222 (mmm) outliers start: 26 outliers final: 13 residues processed: 90 average time/residue: 0.0893 time to fit residues: 12.5148 Evaluate side-chains 76 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 184 ASP 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 51 SER 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 77 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 114 optimal weight: 40.0000 chunk 117 optimal weight: 30.0000 chunk 44 optimal weight: 20.0000 chunk 130 optimal weight: 0.8980 chunk 126 optimal weight: 30.0000 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 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 = 0.4237 r_free = 0.4237 target = 0.115288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.070037 restraints weight = 38220.066| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 6.70 r_work: 0.3031 rms_B_bonded: 5.80 restraints_weight: 2.0000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11467 Z= 0.173 Angle : 0.564 8.201 15548 Z= 0.297 Chirality : 0.045 0.194 1677 Planarity : 0.003 0.036 2002 Dihedral : 4.572 21.051 1517 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.02 % Favored : 94.91 % Rotamer: Outliers : 1.85 % Allowed : 17.75 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.23), residues: 1355 helix: 0.16 (0.42), residues: 170 sheet: 0.04 (0.29), residues: 334 loop : -0.56 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 74 TYR 0.039 0.001 TYR E 24 PHE 0.015 0.001 PHE B 592 TRP 0.043 0.001 TRP B 441 HIS 0.004 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00404 (11443) covalent geometry : angle 0.56164 (15500) SS BOND : bond 0.00374 ( 24) SS BOND : angle 1.15396 ( 48) hydrogen bonds : bond 0.03746 ( 308) hydrogen bonds : angle 5.95569 ( 852) *********************** 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 85 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: B 387 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8280 (pp) REVERT: B 399 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8062 (tpm170) REVERT: A 478 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.5333 (pmt170) REVERT: A 560 ASP cc_start: 0.9129 (m-30) cc_final: 0.8131 (t0) REVERT: A 858 MET cc_start: 0.3984 (tpt) cc_final: 0.3258 (mmm) REVERT: E 53 ASP cc_start: 0.8164 (m-30) cc_final: 0.7891 (p0) outliers start: 23 outliers final: 14 residues processed: 79 average time/residue: 0.1138 time to fit residues: 13.5679 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 : 0.491 ------------------------------------------------------------------------------- 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 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 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 41 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 9 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.114860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.069270 restraints weight = 37779.642| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 6.53 r_work: 0.3022 rms_B_bonded: 5.84 restraints_weight: 2.0000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11467 Z= 0.177 Angle : 0.551 8.124 15548 Z= 0.290 Chirality : 0.045 0.163 1677 Planarity : 0.003 0.035 2002 Dihedral : 4.568 21.094 1517 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.09 % Favored : 94.83 % Rotamer: Outliers : 2.73 % Allowed : 17.35 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.23), residues: 1355 helix: 0.14 (0.41), residues: 172 sheet: 0.03 (0.28), residues: 338 loop : -0.55 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 74 TYR 0.033 0.001 TYR E 24 PHE 0.015 0.001 PHE A 66 TRP 0.044 0.001 TRP B 441 HIS 0.004 0.001 HIS B 456 Details of bonding type rmsd covalent geometry : bond 0.00415 (11443) covalent geometry : angle 0.54814 (15500) SS BOND : bond 0.00367 ( 24) SS BOND : angle 1.21558 ( 48) hydrogen bonds : bond 0.03703 ( 308) hydrogen bonds : angle 5.81088 ( 852) *********************** 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: 34 poor density : 60 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 478 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.5297 (pmt170) REVERT: A 560 ASP cc_start: 0.9146 (m-30) cc_final: 0.8164 (t0) REVERT: A 858 MET cc_start: 0.3999 (tpt) cc_final: 0.3308 (mmm) outliers start: 34 outliers final: 21 residues processed: 86 average time/residue: 0.1034 time to fit residues: 13.4932 Evaluate side-chains 81 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain B residue 399 ARG Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 464 SER 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 430 LEU 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 70 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 45 optimal weight: 0.0970 chunk 84 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ** A 325 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 = 0.4239 r_free = 0.4239 target = 0.115466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.071012 restraints weight = 37729.107| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 5.91 r_work: 0.3047 rms_B_bonded: 5.47 restraints_weight: 2.0000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11467 Z= 0.117 Angle : 0.520 8.324 15548 Z= 0.273 Chirality : 0.044 0.197 1677 Planarity : 0.003 0.034 2002 Dihedral : 4.416 20.073 1517 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.50 % Favored : 95.42 % Rotamer: Outliers : 2.73 % Allowed : 17.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.23), residues: 1355 helix: 0.38 (0.43), residues: 165 sheet: 0.04 (0.28), residues: 357 loop : -0.46 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 821 TYR 0.030 0.001 TYR E 24 PHE 0.015 0.001 PHE B 599 TRP 0.030 0.001 TRP B 441 HIS 0.003 0.001 HIS A 456 Details of bonding type rmsd covalent geometry : bond 0.00269 (11443) covalent geometry : angle 0.51709 (15500) SS BOND : bond 0.00318 ( 24) SS BOND : angle 1.06429 ( 48) hydrogen bonds : bond 0.03409 ( 308) hydrogen bonds : angle 5.63675 ( 852) *********************** 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 96 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 62 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 387 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8173 (pp) REVERT: B 478 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.7111 (mtp85) REVERT: A 478 ARG cc_start: 0.6777 (OUTLIER) cc_final: 0.4313 (ptt180) REVERT: A 560 ASP cc_start: 0.9149 (m-30) cc_final: 0.8146 (t0) outliers start: 34 outliers final: 21 residues processed: 89 average time/residue: 0.1012 time to fit residues: 13.7343 Evaluate side-chains 82 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 464 SER 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 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 514 LEU 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 E residue 23 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 78 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4240 r_free = 0.4240 target = 0.115304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.071667 restraints weight = 37670.951| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 5.89 r_work: 0.3039 rms_B_bonded: 5.39 restraints_weight: 2.0000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11467 Z= 0.140 Angle : 0.539 8.423 15548 Z= 0.281 Chirality : 0.044 0.177 1677 Planarity : 0.003 0.034 2002 Dihedral : 4.450 20.407 1517 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.43 % Favored : 95.42 % Rotamer: Outliers : 2.33 % Allowed : 18.63 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.23), residues: 1355 helix: 0.32 (0.43), residues: 165 sheet: 0.07 (0.28), residues: 357 loop : -0.43 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 821 TYR 0.032 0.001 TYR E 24 PHE 0.011 0.001 PHE B 592 TRP 0.040 0.001 TRP B 441 HIS 0.004 0.001 HIS B 467 Details of bonding type rmsd covalent geometry : bond 0.00328 (11443) covalent geometry : angle 0.53583 (15500) SS BOND : bond 0.00320 ( 24) SS BOND : angle 1.15575 ( 48) hydrogen bonds : bond 0.03432 ( 308) hydrogen bonds : angle 5.61212 ( 852) *********************** 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 90 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 387 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8148 (pp) REVERT: A 478 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.4472 (ptt180) REVERT: A 560 ASP cc_start: 0.9121 (m-30) cc_final: 0.8112 (t0) outliers start: 29 outliers final: 22 residues processed: 85 average time/residue: 0.0928 time to fit residues: 12.3052 Evaluate side-chains 82 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 464 SER 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 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 17 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 791 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.115457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.070160 restraints weight = 37499.863| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 6.45 r_work: 0.3048 rms_B_bonded: 5.76 restraints_weight: 2.0000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11467 Z= 0.121 Angle : 0.541 13.857 15548 Z= 0.279 Chirality : 0.044 0.162 1677 Planarity : 0.003 0.033 2002 Dihedral : 4.374 20.596 1517 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.43 % Favored : 95.50 % Rotamer: Outliers : 2.33 % Allowed : 18.88 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.23), residues: 1355 helix: 0.36 (0.43), residues: 165 sheet: 0.16 (0.28), residues: 352 loop : -0.40 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 821 TYR 0.033 0.001 TYR E 24 PHE 0.014 0.001 PHE B 599 TRP 0.039 0.001 TRP B 441 HIS 0.004 0.001 HIS B 467 Details of bonding type rmsd covalent geometry : bond 0.00280 (11443) covalent geometry : angle 0.53923 (15500) SS BOND : bond 0.00318 ( 24) SS BOND : angle 1.02397 ( 48) hydrogen bonds : bond 0.03312 ( 308) hydrogen bonds : angle 5.50175 ( 852) *********************** 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 89 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 387 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8131 (pp) REVERT: B 469 MET cc_start: 0.7353 (tpp) cc_final: 0.6549 (tpp) REVERT: B 478 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7135 (mtp85) REVERT: A 478 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.6369 (ptp-170) REVERT: A 560 ASP cc_start: 0.9136 (m-30) cc_final: 0.8133 (t0) outliers start: 29 outliers final: 21 residues processed: 83 average time/residue: 0.0957 time to fit residues: 12.4019 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 : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 464 SER 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 624 VAL Chi-restraints excluded: chain B residue 727 SER 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 E residue 23 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 126 optimal weight: 30.0000 chunk 135 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 49 optimal weight: 30.0000 chunk 104 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.115007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.070162 restraints weight = 37591.412| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 6.28 r_work: 0.3044 rms_B_bonded: 5.64 restraints_weight: 2.0000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11467 Z= 0.151 Angle : 0.555 12.815 15548 Z= 0.286 Chirality : 0.044 0.173 1677 Planarity : 0.003 0.033 2002 Dihedral : 4.419 20.732 1517 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.17 % Favored : 94.76 % Rotamer: Outliers : 2.49 % Allowed : 18.88 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.23), residues: 1355 helix: 0.34 (0.43), residues: 166 sheet: 0.25 (0.29), residues: 342 loop : -0.38 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 481 TYR 0.033 0.001 TYR E 24 PHE 0.013 0.001 PHE A 66 TRP 0.040 0.001 TRP B 441 HIS 0.003 0.001 HIS B 456 Details of bonding type rmsd covalent geometry : bond 0.00353 (11443) covalent geometry : angle 0.55266 (15500) SS BOND : bond 0.00319 ( 24) SS BOND : angle 0.99686 ( 48) hydrogen bonds : bond 0.03411 ( 308) hydrogen bonds : angle 5.48123 ( 852) *********************** 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 90 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 59 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 387 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8122 (pp) REVERT: B 469 MET cc_start: 0.7495 (tpp) cc_final: 0.6554 (tpp) REVERT: A 478 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.6463 (ptp-170) REVERT: A 560 ASP cc_start: 0.9139 (m-30) cc_final: 0.8151 (t0) outliers start: 31 outliers final: 25 residues processed: 83 average time/residue: 0.0997 time to fit residues: 12.9609 Evaluate side-chains 86 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 464 SER 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 624 VAL 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 463 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 46 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 110 optimal weight: 20.0000 chunk 77 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.115545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.070414 restraints weight = 37635.614| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 6.41 r_work: 0.3050 rms_B_bonded: 5.79 restraints_weight: 2.0000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11467 Z= 0.111 Angle : 0.536 12.501 15548 Z= 0.276 Chirality : 0.044 0.159 1677 Planarity : 0.003 0.034 2002 Dihedral : 4.317 20.661 1517 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.28 % Favored : 95.65 % Rotamer: Outliers : 2.17 % Allowed : 19.04 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.24), residues: 1355 helix: 0.45 (0.44), residues: 165 sheet: 0.26 (0.28), residues: 361 loop : -0.33 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 56 TYR 0.030 0.001 TYR E 24 PHE 0.015 0.001 PHE B 599 TRP 0.032 0.001 TRP B 441 HIS 0.003 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00257 (11443) covalent geometry : angle 0.53466 (15500) SS BOND : bond 0.00288 ( 24) SS BOND : angle 0.87469 ( 48) hydrogen bonds : bond 0.03207 ( 308) hydrogen bonds : angle 5.40364 ( 852) ********************** 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 88 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 387 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8114 (pp) REVERT: B 469 MET cc_start: 0.7459 (tpp) cc_final: 0.6522 (tpp) REVERT: B 478 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.7086 (mtp85) REVERT: A 478 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.6382 (ptp-170) REVERT: A 560 ASP cc_start: 0.9157 (m-30) cc_final: 0.8145 (t0) REVERT: A 580 MET cc_start: 0.8816 (ttt) cc_final: 0.8615 (mtt) outliers start: 27 outliers final: 21 residues processed: 82 average time/residue: 0.0982 time to fit residues: 12.3236 Evaluate side-chains 84 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 464 SER 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 624 VAL Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain B residue 822 CYS 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 430 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 51 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 114 optimal weight: 50.0000 chunk 111 optimal weight: 0.0050 chunk 95 optimal weight: 0.0980 chunk 126 optimal weight: 30.0000 chunk 100 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.115886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.071028 restraints weight = 38274.069| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 6.37 r_work: 0.3067 rms_B_bonded: 5.79 restraints_weight: 2.0000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11467 Z= 0.102 Angle : 0.531 11.944 15548 Z= 0.273 Chirality : 0.044 0.160 1677 Planarity : 0.003 0.035 2002 Dihedral : 4.219 21.018 1517 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.87 % Favored : 95.06 % Rotamer: Outliers : 2.01 % Allowed : 19.12 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.24), residues: 1355 helix: 0.54 (0.44), residues: 164 sheet: 0.32 (0.28), residues: 357 loop : -0.29 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 581 TYR 0.036 0.001 TYR E 24 PHE 0.010 0.001 PHE A 66 TRP 0.027 0.001 TRP B 441 HIS 0.002 0.000 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00233 (11443) covalent geometry : angle 0.52950 (15500) SS BOND : bond 0.00266 ( 24) SS BOND : angle 0.79843 ( 48) hydrogen bonds : bond 0.03108 ( 308) hydrogen bonds : angle 5.30154 ( 852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5584.94 seconds wall clock time: 95 minutes 42.90 seconds (5742.90 seconds total)