Starting phenix.real_space_refine on Thu Jun 4 15:21:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o1l_70011/06_2026/9o1l_70011_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o1l_70011/06_2026/9o1l_70011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o1l_70011/06_2026/9o1l_70011_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o1l_70011/06_2026/9o1l_70011_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o1l_70011/06_2026/9o1l_70011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o1l_70011/06_2026/9o1l_70011.map" } resolution = 2.91 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= 0.003 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 82 5.16 5 C 8970 2.51 5 N 2146 2.21 5 O 2456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13666 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 6628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6628 Classifications: {'peptide': 806} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 36, 'TRANS': 769} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 205 Unusual residues: {'PGW': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 11 Restraints were copied for chains: A Time building chain proxies: 6.78, per 1000 atoms: 0.50 Number of scatterers: 13666 At special positions: 0 Unit cell: (125.4, 102.3, 116.325, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 12 15.00 O 2456 8.00 N 2146 7.00 C 8970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " 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: 1.18 Conformation dependent library (CDL) restraints added in 601.5 milliseconds 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3076 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 12 sheets defined 58.9% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'B' and resid 90 through 108 Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 188 through 192 removed outlier: 3.648A pdb=" N MET B 192 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 218 Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 293 through 327 removed outlier: 3.742A pdb=" N TYR B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 364 through 375 removed outlier: 3.855A pdb=" N SER B 368 " --> pdb=" O THR B 364 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 409 removed outlier: 3.674A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 425 Processing helix chain 'B' and resid 448 through 456 removed outlier: 3.624A pdb=" N CYS B 456 " --> pdb=" O ARG B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 489 removed outlier: 3.631A pdb=" N TYR B 477 " --> pdb=" O GLY B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 539 removed outlier: 3.539A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 5.333A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 625 Processing helix chain 'B' and resid 625 through 638 Processing helix chain 'B' and resid 648 through 655 removed outlier: 3.702A pdb=" N HIS B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 680 Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.727A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 removed outlier: 4.118A pdb=" N ILE B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 787 through 789 No H-bonds generated for 'chain 'B' and resid 787 through 789' Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 886 removed outlier: 3.581A pdb=" N LEU B 879 " --> pdb=" O THR B 875 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP B 886 " --> pdb=" O SER B 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 108 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 188 through 192 removed outlier: 3.648A pdb=" N MET A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 293 through 327 removed outlier: 3.741A pdb=" N TYR A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 364 through 375 removed outlier: 3.854A pdb=" N SER A 368 " --> pdb=" O THR A 364 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 409 removed outlier: 3.674A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 425 Processing helix chain 'A' and resid 448 through 456 removed outlier: 3.624A pdb=" N CYS A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 489 removed outlier: 3.631A pdb=" N TYR A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 539 removed outlier: 3.538A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 5.332A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 625 Processing helix chain 'A' and resid 625 through 638 Processing helix chain 'A' and resid 648 through 655 removed outlier: 3.702A pdb=" N HIS A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.727A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 4.118A pdb=" N ILE A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 775 through 781 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 825 through 857 Processing helix chain 'A' and resid 861 through 886 removed outlier: 3.580A pdb=" N LEU A 879 " --> pdb=" O THR A 875 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP A 886 " --> pdb=" O SER A 882 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 52 through 53 removed outlier: 4.257A pdb=" N ARG B 116 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 73 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 145 through 150 removed outlier: 6.381A pdb=" N ALA B 185 " --> pdb=" O PRO B 147 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS B 149 " --> pdb=" O PHE B 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 223 through 224 removed outlier: 4.253A pdb=" N GLN B 223 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS B 230 " --> pdb=" O GLN B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 347 through 348 Processing sheet with id=AA5, first strand: chain 'B' and resid 431 through 432 Processing sheet with id=AA6, first strand: chain 'B' and resid 782 through 785 removed outlier: 3.554A pdb=" N TYR B 809 " --> pdb=" O SER B 782 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 52 through 53 removed outlier: 4.257A pdb=" N ARG A 116 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 73 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 145 through 150 removed outlier: 6.381A pdb=" N ALA A 185 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A 149 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 223 through 224 removed outlier: 4.253A pdb=" N GLN A 223 " --> pdb=" O LYS A 230 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 230 " --> pdb=" O GLN A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 347 through 348 Processing sheet with id=AB2, first strand: chain 'A' and resid 431 through 432 Processing sheet with id=AB3, first strand: chain 'A' and resid 782 through 785 removed outlier: 3.554A pdb=" N TYR A 809 " --> pdb=" O SER A 782 " (cutoff:3.500A) 732 hydrogen bonds defined for protein. 2148 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: 2.20 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2106 1.31 - 1.43: 4003 1.43 - 1.56: 7761 1.56 - 1.69: 24 1.69 - 1.82: 124 Bond restraints: 14018 Sorted by residual: bond pdb=" C GLU A 624 " pdb=" N VAL A 625 " ideal model delta sigma weight residual 1.332 1.263 0.069 1.36e-02 5.41e+03 2.60e+01 bond pdb=" C GLU B 624 " pdb=" N VAL B 625 " ideal model delta sigma weight residual 1.332 1.263 0.069 1.36e-02 5.41e+03 2.56e+01 bond pdb=" C1 PGW B1005 " pdb=" O01 PGW B1005 " ideal model delta sigma weight residual 1.332 1.423 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C1 PGW A1005 " pdb=" O01 PGW A1005 " ideal model delta sigma weight residual 1.332 1.423 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C1 PGW A1004 " pdb=" O01 PGW A1004 " ideal model delta sigma weight residual 1.332 1.421 -0.089 2.00e-02 2.50e+03 1.97e+01 ... (remaining 14013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 18417 2.35 - 4.70: 354 4.70 - 7.06: 111 7.06 - 9.41: 26 9.41 - 11.76: 30 Bond angle restraints: 18938 Sorted by residual: angle pdb=" CA GLU B 624 " pdb=" C GLU B 624 " pdb=" N VAL B 625 " ideal model delta sigma weight residual 117.76 123.34 -5.58 1.38e+00 5.25e-01 1.63e+01 angle pdb=" CA GLU A 624 " pdb=" C GLU A 624 " pdb=" N VAL A 625 " ideal model delta sigma weight residual 117.76 123.32 -5.56 1.38e+00 5.25e-01 1.62e+01 angle pdb=" O11 PGW A1001 " pdb=" P PGW A1001 " pdb=" O12 PGW A1001 " ideal model delta sigma weight residual 98.90 109.91 -11.01 3.00e+00 1.11e-01 1.35e+01 angle pdb=" O11 PGW B1001 " pdb=" P PGW B1001 " pdb=" O12 PGW B1001 " ideal model delta sigma weight residual 98.90 109.91 -11.01 3.00e+00 1.11e-01 1.35e+01 angle pdb=" O11 PGW B1002 " pdb=" P PGW B1002 " pdb=" O12 PGW B1002 " ideal model delta sigma weight residual 98.90 109.67 -10.77 3.00e+00 1.11e-01 1.29e+01 ... (remaining 18933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.84: 7918 33.84 - 67.68: 436 67.68 - 101.53: 40 101.53 - 135.37: 20 135.37 - 169.21: 4 Dihedral angle restraints: 8418 sinusoidal: 3638 harmonic: 4780 Sorted by residual: dihedral pdb=" CB CYS A 331 " pdb=" SG CYS A 331 " pdb=" SG CYS A 372 " pdb=" CB CYS A 372 " ideal model delta sinusoidal sigma weight residual -86.00 -166.20 80.20 1 1.00e+01 1.00e-02 7.97e+01 dihedral pdb=" CB CYS B 331 " pdb=" SG CYS B 331 " pdb=" SG CYS B 372 " pdb=" CB CYS B 372 " ideal model delta sinusoidal sigma weight residual -86.00 -166.18 80.18 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" CB CYS A 352 " pdb=" SG CYS A 352 " pdb=" SG CYS A 356 " pdb=" CB CYS A 356 " ideal model delta sinusoidal sigma weight residual -86.00 -17.63 -68.37 1 1.00e+01 1.00e-02 6.06e+01 ... (remaining 8415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1366 0.036 - 0.073: 491 0.073 - 0.109: 139 0.109 - 0.145: 20 0.145 - 0.182: 12 Chirality restraints: 2028 Sorted by residual: chirality pdb=" C02 PGW A1003 " pdb=" C01 PGW A1003 " pdb=" C03 PGW A1003 " pdb=" O01 PGW A1003 " both_signs ideal model delta sigma weight residual False 2.36 2.54 -0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" C02 PGW B1003 " pdb=" C01 PGW B1003 " pdb=" C03 PGW B1003 " pdb=" O01 PGW B1003 " both_signs ideal model delta sigma weight residual False 2.36 2.54 -0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" C02 PGW A1001 " pdb=" C01 PGW A1001 " pdb=" C03 PGW A1001 " pdb=" O01 PGW A1001 " both_signs ideal model delta sigma weight residual False 2.36 2.54 -0.18 2.00e-01 2.50e+01 8.01e-01 ... (remaining 2025 not shown) Planarity restraints: 2348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 504 " 0.082 5.00e-02 4.00e+02 1.23e-01 2.44e+01 pdb=" N PRO B 505 " -0.213 5.00e-02 4.00e+02 pdb=" CA PRO B 505 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 505 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 504 " -0.082 5.00e-02 4.00e+02 1.23e-01 2.43e+01 pdb=" N PRO A 505 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO A 505 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 505 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 629 " 0.018 2.00e-02 2.50e+03 1.74e-02 7.60e+00 pdb=" CG TRP A 629 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 629 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 629 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 629 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 629 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 629 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 629 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 629 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 629 " -0.000 2.00e-02 2.50e+03 ... (remaining 2345 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 512 2.72 - 3.27: 13404 3.27 - 3.81: 22828 3.81 - 4.36: 27053 4.36 - 4.90: 46989 Nonbonded interactions: 110786 Sorted by model distance: nonbonded pdb=" O ASP B 749 " pdb=" OD1 ASP B 749 " model vdw 2.178 3.040 nonbonded pdb=" O ASP A 749 " pdb=" OD1 ASP A 749 " model vdw 2.179 3.040 nonbonded pdb=" OD1 ASN A 205 " pdb=" N THR A 208 " model vdw 2.212 3.120 nonbonded pdb=" OD1 ASN B 205 " pdb=" N THR B 208 " model vdw 2.212 3.120 nonbonded pdb=" OG SER B 117 " pdb=" O ASP B 120 " model vdw 2.243 3.040 ... (remaining 110781 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.070 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:7.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 0.091 14028 Z= 0.258 Angle : 0.922 11.762 18958 Z= 0.373 Chirality : 0.042 0.182 2028 Planarity : 0.005 0.123 2348 Dihedral : 20.966 169.209 5312 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.42 % Allowed : 26.32 % Favored : 73.27 % 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 are not related in a simple way. whole: 1.34 (0.21), residues: 1600 helix: 2.21 (0.17), residues: 872 sheet: 0.25 (0.51), residues: 102 loop : -0.95 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 235 TYR 0.018 0.001 TYR B 323 PHE 0.012 0.001 PHE A 560 TRP 0.046 0.001 TRP A 629 HIS 0.008 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.26 (14018) covalent geometry : angle 0.92073 / 0.37 (18938) SS BOND : bond 0.00244 / 0.12 ( 10) SS BOND : angle 1.52444 / 0.88 ( 20) hydrogen bonds : bond 0.12171 / 7.87 ( 732) hydrogen bonds : angle 5.56656 / 3.85 ( 2148) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 166 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 770 TYR cc_start: 0.7325 (t80) cc_final: 0.7112 (t80) REVERT: A 52 PHE cc_start: 0.7483 (m-80) cc_final: 0.6976 (m-80) REVERT: A 870 ARG cc_start: 0.6137 (tpt170) cc_final: 0.5916 (ttt-90) outliers start: 6 outliers final: 6 residues processed: 172 average time/residue: 0.4877 time to fit residues: 93.8155 Evaluate side-chains 154 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 789 PHE Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 789 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN B 99 GLN B 223 GLN B 415 GLN B 418 GLN B 429 HIS B 710 GLN B 796 ASN B 883 HIS A 86 ASN A 99 GLN A 223 GLN A 415 GLN A 418 GLN A 429 HIS A 710 GLN A 796 ASN A 883 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.189970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.123365 restraints weight = 14813.742| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.54 r_work: 0.3412 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14028 Z= 0.128 Angle : 0.537 11.348 18958 Z= 0.272 Chirality : 0.041 0.160 2028 Planarity : 0.005 0.082 2348 Dihedral : 18.353 178.280 2130 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.44 % Favored : 96.44 % Rotamer: Outliers : 3.81 % Allowed : 24.03 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.21), residues: 1600 helix: 2.20 (0.17), residues: 882 sheet: 0.46 (0.54), residues: 102 loop : -0.87 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 592 TYR 0.017 0.001 TYR A 323 PHE 0.012 0.001 PHE A 560 TRP 0.017 0.001 TRP B 629 HIS 0.007 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (14018) covalent geometry : angle 0.53206 / 0.27 (18938) SS BOND : bond 0.00226 / 0.10 ( 10) SS BOND : angle 2.26501 / 1.34 ( 20) hydrogen bonds : bond 0.04376 / 2.84 ( 732) hydrogen bonds : angle 4.40080 / 3.06 ( 2148) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 161 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 235 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7494 (ptm160) REVERT: B 659 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8089 (tpp) REVERT: B 770 TYR cc_start: 0.7360 (t80) cc_final: 0.7153 (t80) REVERT: B 842 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7396 (ttt) REVERT: A 235 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7540 (ptm160) REVERT: A 659 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8226 (tpp) REVERT: A 842 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7410 (ttt) outliers start: 55 outliers final: 18 residues processed: 191 average time/residue: 0.4853 time to fit residues: 103.1984 Evaluate side-chains 167 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 789 PHE Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 860 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 119 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 101 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 418 GLN B 429 HIS A 418 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.193672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.125854 restraints weight = 14936.471| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.60 r_work: 0.3418 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14028 Z= 0.108 Angle : 0.516 8.909 18958 Z= 0.264 Chirality : 0.040 0.157 2028 Planarity : 0.005 0.069 2348 Dihedral : 16.952 171.856 2126 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.44 % Favored : 96.44 % Rotamer: Outliers : 3.25 % Allowed : 25.00 % Favored : 71.75 % 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 are not related in a simple way. whole: 1.48 (0.21), residues: 1600 helix: 2.25 (0.17), residues: 882 sheet: 0.65 (0.55), residues: 102 loop : -0.90 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 870 TYR 0.019 0.001 TYR A 77 PHE 0.013 0.001 PHE B 560 TRP 0.015 0.001 TRP B 629 HIS 0.012 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (14018) covalent geometry : angle 0.51052 / 0.26 (18938) SS BOND : bond 0.00279 / 0.12 ( 10) SS BOND : angle 2.32654 / 1.34 ( 20) hydrogen bonds : bond 0.04081 / 2.66 ( 732) hydrogen bonds : angle 4.28769 / 2.98 ( 2148) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 GLU cc_start: 0.7401 (mt-10) cc_final: 0.6794 (tm-30) REVERT: B 659 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8106 (tpp) REVERT: B 842 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7282 (ttt) REVERT: A 472 ILE cc_start: 0.8394 (mt) cc_final: 0.8131 (mt) REVERT: A 555 MET cc_start: 0.8692 (mmt) cc_final: 0.8337 (mmt) REVERT: A 659 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8152 (tpp) REVERT: A 842 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7342 (ttt) outliers start: 47 outliers final: 27 residues processed: 180 average time/residue: 0.4977 time to fit residues: 100.0853 Evaluate side-chains 178 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 789 PHE Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 860 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 154 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 60 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 418 GLN A 418 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.193613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.125600 restraints weight = 14959.328| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.61 r_work: 0.3412 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14028 Z= 0.110 Angle : 0.521 13.011 18958 Z= 0.263 Chirality : 0.040 0.152 2028 Planarity : 0.005 0.064 2348 Dihedral : 16.023 171.975 2126 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.12 % Favored : 96.75 % Rotamer: Outliers : 3.46 % Allowed : 24.31 % Favored : 72.23 % 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 are not related in a simple way. whole: 1.49 (0.21), residues: 1600 helix: 2.27 (0.17), residues: 882 sheet: 0.69 (0.56), residues: 102 loop : -0.91 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 870 TYR 0.012 0.001 TYR B 306 PHE 0.012 0.001 PHE A 560 TRP 0.017 0.001 TRP B 629 HIS 0.005 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (14018) covalent geometry : angle 0.51646 / 0.26 (18938) SS BOND : bond 0.00141 / 0.07 ( 10) SS BOND : angle 2.11386 / 1.22 ( 20) hydrogen bonds : bond 0.03991 / 2.60 ( 732) hydrogen bonds : angle 4.23598 / 2.95 ( 2148) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 154 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6783 (tm-30) REVERT: B 555 MET cc_start: 0.8780 (mmt) cc_final: 0.8299 (mmt) REVERT: B 659 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8094 (tpp) REVERT: B 842 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7295 (ttt) REVERT: A 235 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7517 (ptm160) REVERT: A 472 ILE cc_start: 0.8431 (mt) cc_final: 0.8148 (mt) REVERT: A 555 MET cc_start: 0.8711 (mmt) cc_final: 0.8406 (mmt) REVERT: A 659 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8202 (tpp) REVERT: A 842 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7364 (ttt) outliers start: 50 outliers final: 29 residues processed: 184 average time/residue: 0.5199 time to fit residues: 106.6619 Evaluate side-chains 179 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 789 PHE Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 860 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 chunk 135 optimal weight: 40.0000 chunk 16 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 418 GLN B 652 GLN A 418 GLN A 652 GLN A 818 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.186955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.120535 restraints weight = 15054.563| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.51 r_work: 0.3339 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14028 Z= 0.228 Angle : 0.610 14.206 18958 Z= 0.310 Chirality : 0.044 0.143 2028 Planarity : 0.005 0.065 2348 Dihedral : 15.912 173.399 2126 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.62 % Favored : 96.25 % Rotamer: Outliers : 4.57 % Allowed : 23.20 % Favored : 72.23 % 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 are not related in a simple way. whole: 1.07 (0.21), residues: 1600 helix: 1.94 (0.16), residues: 890 sheet: 0.38 (0.53), residues: 102 loop : -1.13 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 870 TYR 0.018 0.002 TYR B 306 PHE 0.015 0.001 PHE B 560 TRP 0.019 0.002 TRP B 629 HIS 0.006 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.23 (14018) covalent geometry : angle 0.60460 / 0.31 (18938) SS BOND : bond 0.00372 / 0.18 ( 10) SS BOND : angle 2.52199 / 1.44 ( 20) hydrogen bonds : bond 0.05109 / 3.33 ( 732) hydrogen bonds : angle 4.42208 / 3.09 ( 2148) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 140 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8372 (t80) REVERT: B 211 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6869 (ttp-170) REVERT: B 256 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7378 (mm-30) REVERT: B 329 ASP cc_start: 0.7754 (t0) cc_final: 0.7546 (t0) REVERT: B 538 PHE cc_start: 0.8038 (t80) cc_final: 0.7826 (t80) REVERT: B 555 MET cc_start: 0.8919 (mmt) cc_final: 0.8524 (mmt) REVERT: B 659 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8306 (tpp) REVERT: B 842 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7705 (ttt) REVERT: A 73 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8320 (t80) REVERT: A 211 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6879 (ttp-170) REVERT: A 235 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7589 (ptm160) REVERT: A 424 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7197 (mm-30) REVERT: A 538 PHE cc_start: 0.8079 (t80) cc_final: 0.7878 (t80) REVERT: A 555 MET cc_start: 0.8943 (mmt) cc_final: 0.8574 (mmt) REVERT: A 659 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8360 (tpp) REVERT: A 842 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7772 (ttt) outliers start: 66 outliers final: 19 residues processed: 178 average time/residue: 0.5109 time to fit residues: 100.9000 Evaluate side-chains 161 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 789 PHE Chi-restraints excluded: chain B residue 823 LYS Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 842 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 87 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 119 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 418 GLN A 418 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.186527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.118395 restraints weight = 14998.054| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.58 r_work: 0.3333 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14028 Z= 0.136 Angle : 0.559 14.751 18958 Z= 0.284 Chirality : 0.041 0.149 2028 Planarity : 0.005 0.060 2348 Dihedral : 15.274 172.648 2126 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.31 % Favored : 96.56 % Rotamer: Outliers : 3.74 % Allowed : 24.24 % Favored : 72.02 % 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 are not related in a simple way. whole: 1.18 (0.21), residues: 1600 helix: 2.02 (0.17), residues: 882 sheet: 0.41 (0.55), residues: 102 loop : -1.02 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 870 TYR 0.017 0.001 TYR A 323 PHE 0.021 0.001 PHE A 358 TRP 0.019 0.001 TRP B 629 HIS 0.004 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (14018) covalent geometry : angle 0.55259 / 0.28 (18938) SS BOND : bond 0.00167 / 0.08 ( 10) SS BOND : angle 2.62765 / 1.50 ( 20) hydrogen bonds : bond 0.04340 / 2.83 ( 732) hydrogen bonds : angle 4.36391 / 3.04 ( 2148) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 153 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8137 (t80) REVERT: B 256 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7234 (mm-30) REVERT: B 327 ASP cc_start: 0.8269 (t0) cc_final: 0.8035 (t0) REVERT: B 429 HIS cc_start: 0.6301 (OUTLIER) cc_final: 0.5885 (t70) REVERT: B 538 PHE cc_start: 0.7962 (t80) cc_final: 0.5888 (m-10) REVERT: B 555 MET cc_start: 0.8797 (mmt) cc_final: 0.8462 (mmt) REVERT: B 659 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8150 (tpp) REVERT: B 842 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7378 (ttt) REVERT: A 73 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8128 (t80) REVERT: A 211 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6713 (ttp-170) REVERT: A 235 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7540 (ptm160) REVERT: A 538 PHE cc_start: 0.8003 (t80) cc_final: 0.5944 (m-10) REVERT: A 555 MET cc_start: 0.8795 (mmt) cc_final: 0.8585 (mmt) REVERT: A 659 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8163 (tpp) REVERT: A 842 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7470 (ttt) outliers start: 54 outliers final: 20 residues processed: 187 average time/residue: 0.4715 time to fit residues: 98.8203 Evaluate side-chains 174 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 789 PHE Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 842 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 84 optimal weight: 30.0000 chunk 96 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 137 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 418 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.183955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117237 restraints weight = 15008.281| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.51 r_work: 0.3311 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14028 Z= 0.179 Angle : 0.603 15.516 18958 Z= 0.304 Chirality : 0.043 0.144 2028 Planarity : 0.005 0.062 2348 Dihedral : 15.192 174.011 2126 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.88 % Favored : 96.00 % Rotamer: Outliers : 3.53 % Allowed : 25.07 % Favored : 71.40 % 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 are not related in a simple way. whole: 1.10 (0.21), residues: 1600 helix: 2.01 (0.16), residues: 876 sheet: 0.29 (0.54), residues: 102 loop : -1.12 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 219 TYR 0.016 0.001 TYR B 306 PHE 0.017 0.001 PHE A 358 TRP 0.021 0.002 TRP B 629 HIS 0.005 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 (14018) covalent geometry : angle 0.59571 / 0.30 (18938) SS BOND : bond 0.00286 / 0.14 ( 10) SS BOND : angle 2.89582 / 1.65 ( 20) hydrogen bonds : bond 0.04704 / 3.07 ( 732) hydrogen bonds : angle 4.43590 / 3.09 ( 2148) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 140 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8158 (t80) REVERT: B 256 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7250 (mm-30) REVERT: B 424 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7247 (mm-30) REVERT: B 429 HIS cc_start: 0.6362 (OUTLIER) cc_final: 0.5932 (t70) REVERT: B 555 MET cc_start: 0.8844 (mmt) cc_final: 0.8521 (mmt) REVERT: B 659 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8163 (tpp) REVERT: B 842 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7497 (ttt) REVERT: A 73 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8133 (t80) REVERT: A 148 LEU cc_start: 0.4449 (OUTLIER) cc_final: 0.4200 (pp) REVERT: A 211 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6694 (ttp-170) REVERT: A 235 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7588 (ptm160) REVERT: A 555 MET cc_start: 0.8849 (mmt) cc_final: 0.8608 (mmt) REVERT: A 659 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8195 (tpp) REVERT: A 842 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7528 (ttt) outliers start: 51 outliers final: 23 residues processed: 173 average time/residue: 0.4869 time to fit residues: 93.9890 Evaluate side-chains 170 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 789 PHE Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 823 LYS Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 842 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 47 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 136 optimal weight: 0.0170 chunk 111 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 418 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.188966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.119144 restraints weight = 14940.169| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.65 r_work: 0.3322 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14028 Z= 0.146 Angle : 0.584 14.889 18958 Z= 0.293 Chirality : 0.041 0.145 2028 Planarity : 0.005 0.061 2348 Dihedral : 14.902 174.195 2126 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.44 % Favored : 96.44 % Rotamer: Outliers : 3.46 % Allowed : 25.35 % Favored : 71.19 % 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 are not related in a simple way. whole: 1.18 (0.21), residues: 1600 helix: 2.09 (0.17), residues: 874 sheet: 0.33 (0.54), residues: 102 loop : -1.09 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 219 TYR 0.020 0.001 TYR A 323 PHE 0.017 0.001 PHE B 358 TRP 0.022 0.001 TRP B 629 HIS 0.004 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (14018) covalent geometry : angle 0.57816 / 0.29 (18938) SS BOND : bond 0.00228 / 0.11 ( 10) SS BOND : angle 2.56461 / 1.47 ( 20) hydrogen bonds : bond 0.04411 / 2.89 ( 732) hydrogen bonds : angle 4.38366 / 3.05 ( 2148) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 146 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.8094 (t80) REVERT: B 256 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7218 (mm-30) REVERT: B 424 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7183 (mm-30) REVERT: B 555 MET cc_start: 0.8781 (mmt) cc_final: 0.8417 (mmt) REVERT: B 659 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8148 (tpp) REVERT: B 842 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7370 (ttt) REVERT: A 73 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8072 (t80) REVERT: A 148 LEU cc_start: 0.4468 (OUTLIER) cc_final: 0.4217 (pp) REVERT: A 211 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6652 (ttp-170) REVERT: A 235 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7551 (ptm160) REVERT: A 555 MET cc_start: 0.8794 (mmt) cc_final: 0.8591 (mmt) REVERT: A 659 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8158 (tpp) REVERT: A 842 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7428 (ttt) outliers start: 50 outliers final: 23 residues processed: 178 average time/residue: 0.4910 time to fit residues: 97.7719 Evaluate side-chains 171 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 789 PHE Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 860 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 24 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 418 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.184122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.116292 restraints weight = 14983.269| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.55 r_work: 0.3302 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14028 Z= 0.192 Angle : 0.629 17.115 18958 Z= 0.315 Chirality : 0.043 0.141 2028 Planarity : 0.005 0.062 2348 Dihedral : 15.005 175.295 2126 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.81 % Favored : 96.06 % Rotamer: Outliers : 2.84 % Allowed : 25.97 % Favored : 71.19 % 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 are not related in a simple way. whole: 1.02 (0.21), residues: 1600 helix: 1.96 (0.16), residues: 874 sheet: 0.17 (0.53), residues: 102 loop : -1.14 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 219 TYR 0.016 0.001 TYR B 306 PHE 0.017 0.001 PHE A 358 TRP 0.023 0.002 TRP B 629 HIS 0.011 0.001 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.19 (14018) covalent geometry : angle 0.62249 / 0.31 (18938) SS BOND : bond 0.00311 / 0.15 ( 10) SS BOND : angle 2.91346 / 1.67 ( 20) hydrogen bonds : bond 0.04781 / 3.13 ( 732) hydrogen bonds : angle 4.47338 / 3.12 ( 2148) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8180 (t80) REVERT: B 256 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7265 (mm-30) REVERT: B 424 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7265 (mm-30) REVERT: B 555 MET cc_start: 0.8853 (mmt) cc_final: 0.8507 (mmt) REVERT: B 659 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8215 (tpp) REVERT: B 842 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7504 (ttt) REVERT: A 73 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8157 (t80) REVERT: A 148 LEU cc_start: 0.4456 (OUTLIER) cc_final: 0.4192 (pp) REVERT: A 211 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6730 (ttp-170) REVERT: A 659 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8231 (tpp) REVERT: A 842 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7551 (ttt) outliers start: 41 outliers final: 21 residues processed: 159 average time/residue: 0.5115 time to fit residues: 90.5634 Evaluate side-chains 161 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 789 PHE Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 823 LYS Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 842 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 61 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 97 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 418 GLN A 418 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.189565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.120641 restraints weight = 14827.625| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.61 r_work: 0.3341 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14028 Z= 0.123 Angle : 0.585 16.550 18958 Z= 0.291 Chirality : 0.041 0.145 2028 Planarity : 0.005 0.063 2348 Dihedral : 14.621 175.592 2126 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.38 % Favored : 96.50 % Rotamer: Outliers : 2.15 % Allowed : 26.66 % Favored : 71.19 % 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 are not related in a simple way. whole: 1.27 (0.21), residues: 1600 helix: 2.17 (0.17), residues: 868 sheet: 0.35 (0.54), residues: 102 loop : -1.02 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 219 TYR 0.013 0.001 TYR A 580 PHE 0.017 0.001 PHE A 358 TRP 0.023 0.001 TRP B 629 HIS 0.005 0.001 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (14018) covalent geometry : angle 0.58080 / 0.29 (18938) SS BOND : bond 0.00171 / 0.08 ( 10) SS BOND : angle 2.30138 / 1.31 ( 20) hydrogen bonds : bond 0.04158 / 2.72 ( 732) hydrogen bonds : angle 4.35826 / 3.03 ( 2148) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8101 (t80) REVERT: B 256 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7209 (mm-30) REVERT: B 424 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7224 (mm-30) REVERT: B 538 PHE cc_start: 0.7893 (t80) cc_final: 0.5856 (m-10) REVERT: B 842 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7287 (ttt) REVERT: A 73 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8094 (t80) REVERT: A 148 LEU cc_start: 0.4361 (OUTLIER) cc_final: 0.4093 (pp) REVERT: A 256 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7299 (mm-30) REVERT: A 538 PHE cc_start: 0.7891 (t80) cc_final: 0.5845 (m-10) REVERT: A 555 MET cc_start: 0.8666 (mmt) cc_final: 0.8457 (mmt) REVERT: A 842 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7384 (ttt) outliers start: 31 outliers final: 21 residues processed: 168 average time/residue: 0.5092 time to fit residues: 95.7073 Evaluate side-chains 168 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 789 PHE Chi-restraints excluded: chain B residue 823 LYS Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 842 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 62 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 113 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 30.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 418 GLN B 433 ASN A 418 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.186040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.118304 restraints weight = 15015.975| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.57 r_work: 0.3331 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14028 Z= 0.149 Angle : 0.599 16.340 18958 Z= 0.298 Chirality : 0.042 0.142 2028 Planarity : 0.005 0.066 2348 Dihedral : 14.633 176.429 2126 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.62 % Favored : 96.25 % Rotamer: Outliers : 2.35 % Allowed : 26.59 % Favored : 71.05 % 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 are not related in a simple way. whole: 1.20 (0.21), residues: 1600 helix: 2.10 (0.17), residues: 874 sheet: 0.33 (0.54), residues: 102 loop : -1.08 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 870 TYR 0.020 0.001 TYR A 323 PHE 0.015 0.001 PHE B 358 TRP 0.023 0.002 TRP B 629 HIS 0.005 0.001 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (14018) covalent geometry : angle 0.59391 / 0.30 (18938) SS BOND : bond 0.00206 / 0.10 ( 10) SS BOND : angle 2.49432 / 1.43 ( 20) hydrogen bonds : bond 0.04355 / 2.85 ( 732) hydrogen bonds : angle 4.38928 / 3.06 ( 2148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4155.37 seconds wall clock time: 71 minutes 44.34 seconds (4304.34 seconds total)