Starting phenix.real_space_refine on Thu Jun 4 13:51:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o1o_70014/06_2026/9o1o_70014.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o1o_70014/06_2026/9o1o_70014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o1o_70014/06_2026/9o1o_70014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o1o_70014/06_2026/9o1o_70014.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o1o_70014/06_2026/9o1o_70014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o1o_70014/06_2026/9o1o_70014.map" } resolution = 2.97 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= 0.033 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 P 6 5.49 5 S 82 5.16 5 C 8660 2.51 5 N 2102 2.21 5 O 2354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 13210 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 6491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6491 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 36, 'TRANS': 752} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 114 Unusual residues: {' CA': 3, 'PGW': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGW:plan-3': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: A Time building chain proxies: 5.49, per 1000 atoms: 0.42 Number of scatterers: 13210 At special positions: 0 Unit cell: (91.575, 122.925, 121.275, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 82 16.00 P 6 15.00 O 2354 8.00 N 2102 7.00 C 8660 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: 1.01 Conformation dependent library (CDL) restraints added in 427.4 milliseconds 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3008 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 10 sheets defined 60.3% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'B' and resid 89 through 103 removed outlier: 3.614A pdb=" N LYS B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 94 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 142 removed outlier: 3.535A pdb=" N MET B 142 " --> pdb=" O TYR B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.857A pdb=" N VAL B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 240 removed outlier: 3.501A pdb=" N GLY B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 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 328 removed outlier: 3.513A pdb=" N TYR B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.603A 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 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 363 through 370 removed outlier: 4.724A pdb=" N SER B 367 " --> pdb=" O ILE B 363 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 409 removed outlier: 3.602A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 426 Processing helix chain 'B' and resid 448 through 456 Processing helix chain 'B' and resid 456 through 489 removed outlier: 3.567A pdb=" N TYR B 477 " --> pdb=" O GLY B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 539 removed outlier: 3.984A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 5.319A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 638 removed outlier: 3.606A pdb=" N VAL B 625 " --> pdb=" O ASN B 621 " (cutoff:3.500A) Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 655 Processing helix chain 'B' and resid 664 through 681 removed outlier: 3.765A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.560A pdb=" N LEU B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 removed outlier: 3.991A pdb=" N ILE B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 759 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 796 through 802 removed outlier: 3.527A pdb=" N ILE B 799 " --> pdb=" O ASN B 796 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 801 " --> pdb=" O TYR B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 886 Processing helix chain 'A' and resid 89 through 103 removed outlier: 3.614A pdb=" N LYS A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 142 removed outlier: 3.535A pdb=" N MET A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 205 through 220 removed outlier: 3.857A pdb=" N VAL A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 240 removed outlier: 3.501A pdb=" N GLY A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 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 328 removed outlier: 3.512A pdb=" N TYR A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.604A 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 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 363 through 370 removed outlier: 4.723A pdb=" N SER A 367 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 409 removed outlier: 3.602A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'A' and resid 456 through 489 removed outlier: 3.568A pdb=" N TYR A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 539 removed outlier: 3.984A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 5.318A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 638 removed outlier: 3.607A pdb=" N VAL A 625 " --> pdb=" O ASN A 621 " (cutoff:3.500A) Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 664 through 681 removed outlier: 3.764A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.560A pdb=" N LEU A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.991A pdb=" N ILE A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 759 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 796 through 802 removed outlier: 3.527A pdb=" N ILE A 799 " --> pdb=" O ASN A 796 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 801 " --> pdb=" O TYR A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 Processing helix chain 'A' and resid 861 through 886 Processing sheet with id=AA1, first strand: chain 'B' and resid 51 through 52 removed outlier: 6.821A pdb=" N GLU B 51 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N ARG B 116 " --> pdb=" O GLU B 51 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE B 73 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.136A 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 147 Processing sheet with id=AA3, first strand: chain 'B' and resid 223 through 224 Processing sheet with id=AA4, first strand: chain 'B' and resid 429 through 432 Processing sheet with id=AA5, first strand: chain 'B' and resid 782 through 785 Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.821A pdb=" N GLU A 51 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N ARG A 116 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A 73 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA8, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AA9, first strand: chain 'A' and resid 429 through 432 Processing sheet with id=AB1, first strand: chain 'A' and resid 782 through 785 734 hydrogen bonds defined for protein. 2142 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: 1.95 Time building geometry restraints manager: 1.28 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: 2046 1.31 - 1.44: 3889 1.44 - 1.56: 7483 1.56 - 1.69: 12 1.69 - 1.82: 124 Bond restraints: 13554 Sorted by residual: bond pdb=" C19 PGW A1004 " pdb=" O03 PGW A1004 " ideal model delta sigma weight residual 1.332 1.466 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C19 PGW B1004 " pdb=" O03 PGW B1004 " ideal model delta sigma weight residual 1.332 1.465 -0.133 2.00e-02 2.50e+03 4.43e+01 bond pdb=" C1 PGW B1004 " pdb=" O01 PGW B1004 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C1 PGW A1004 " pdb=" O01 PGW A1004 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" C1 PGW A1005 " pdb=" O01 PGW A1005 " ideal model delta sigma weight residual 1.332 1.452 -0.120 2.00e-02 2.50e+03 3.58e+01 ... (remaining 13549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 18041 2.73 - 5.45: 229 5.45 - 8.18: 46 8.18 - 10.91: 20 10.91 - 13.63: 4 Bond angle restraints: 18340 Sorted by residual: angle pdb=" C20 PGW B1005 " pdb=" C19 PGW B1005 " pdb=" O03 PGW B1005 " ideal model delta sigma weight residual 111.03 124.66 -13.63 3.00e+00 1.11e-01 2.06e+01 angle pdb=" C20 PGW A1005 " pdb=" C19 PGW A1005 " pdb=" O03 PGW A1005 " ideal model delta sigma weight residual 111.03 124.65 -13.62 3.00e+00 1.11e-01 2.06e+01 angle pdb=" C TYR A 666 " pdb=" N GLU A 667 " pdb=" CA GLU A 667 " ideal model delta sigma weight residual 120.29 126.03 -5.74 1.42e+00 4.96e-01 1.64e+01 angle pdb=" C TYR B 666 " pdb=" N GLU B 667 " pdb=" CA GLU B 667 " ideal model delta sigma weight residual 120.29 126.01 -5.72 1.42e+00 4.96e-01 1.63e+01 angle pdb=" N GLU B 424 " pdb=" CA GLU B 424 " pdb=" C GLU B 424 " ideal model delta sigma weight residual 111.07 106.77 4.30 1.07e+00 8.73e-01 1.61e+01 ... (remaining 18335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.90: 7708 33.90 - 67.81: 344 67.81 - 101.71: 36 101.71 - 135.62: 6 135.62 - 169.52: 4 Dihedral angle restraints: 8098 sinusoidal: 3424 harmonic: 4674 Sorted by residual: 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 -156.18 70.18 1 1.00e+01 1.00e-02 6.34e+01 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 -156.17 70.17 1 1.00e+01 1.00e-02 6.34e+01 dihedral pdb=" O12 PGW A1006 " pdb=" C04 PGW A1006 " pdb=" C05 PGW A1006 " pdb=" OAF PGW A1006 " ideal model delta sinusoidal sigma weight residual 69.27 -121.21 -169.52 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 8095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1694 0.058 - 0.115: 260 0.115 - 0.173: 22 0.173 - 0.230: 2 0.230 - 0.288: 2 Chirality restraints: 1980 Sorted by residual: chirality pdb=" C02 PGW A1004 " pdb=" C01 PGW A1004 " pdb=" C03 PGW A1004 " pdb=" O01 PGW A1004 " both_signs ideal model delta sigma weight residual False 2.36 2.64 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C02 PGW B1004 " pdb=" C01 PGW B1004 " pdb=" C03 PGW B1004 " pdb=" O01 PGW B1004 " both_signs ideal model delta sigma weight residual False 2.36 2.64 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C02 PGW B1005 " pdb=" C01 PGW B1005 " pdb=" C03 PGW B1005 " pdb=" O01 PGW B1005 " both_signs ideal model delta sigma weight residual False 2.36 2.56 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1977 not shown) Planarity restraints: 2282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 762 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.50e+00 pdb=" N PRO A 763 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 763 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 763 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 762 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO B 763 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 763 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 763 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 666 " -0.012 2.00e-02 2.50e+03 2.52e-02 6.36e+00 pdb=" C TYR A 666 " 0.044 2.00e-02 2.50e+03 pdb=" O TYR A 666 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU A 667 " -0.015 2.00e-02 2.50e+03 ... (remaining 2279 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3069 2.78 - 3.31: 12410 3.31 - 3.84: 22118 3.84 - 4.37: 24602 4.37 - 4.90: 44035 Nonbonded interactions: 106234 Sorted by model distance: nonbonded pdb=" OE2 GLU B 478 " pdb=" OH TYR B 569 " model vdw 2.255 3.040 nonbonded pdb=" OE2 GLU A 478 " pdb=" OH TYR A 569 " model vdw 2.255 3.040 nonbonded pdb=" O ILE A 744 " pdb=" OG SER A 748 " model vdw 2.271 3.040 nonbonded pdb=" O ILE B 744 " pdb=" OG SER B 748 " model vdw 2.272 3.040 nonbonded pdb=" OE1 GLU A 699 " pdb="CA CA A1001 " model vdw 2.291 2.510 ... (remaining 106229 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: 0.01 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: 1.040 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.230 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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 0.134 13564 Z= 0.238 Angle : 0.772 13.633 18360 Z= 0.347 Chirality : 0.041 0.288 1980 Planarity : 0.005 0.064 2282 Dihedral : 18.708 169.522 5060 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.42 % Allowed : 22.03 % Favored : 77.54 % 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: 1.79 (0.21), residues: 1562 helix: 2.36 (0.17), residues: 910 sheet: 0.07 (0.60), residues: 78 loop : -0.60 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 98 TYR 0.030 0.001 TYR B 77 PHE 0.012 0.001 PHE B 393 TRP 0.014 0.001 TRP A 132 HIS 0.002 0.000 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.24 (13554) covalent geometry : angle 0.77205 / 0.35 (18340) SS BOND : bond 0.00153 / 0.07 ( 10) SS BOND : angle 0.70634 / 0.43 ( 20) hydrogen bonds : bond 0.10263 / 6.96 ( 734) hydrogen bonds : angle 4.65915 / 3.18 ( 2142) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 ARG cc_start: 0.7874 (ttt90) cc_final: 0.6326 (tmm160) REVERT: A 235 ARG cc_start: 0.7840 (ttt90) cc_final: 0.6412 (tmm160) outliers start: 6 outliers final: 5 residues processed: 159 average time/residue: 0.4422 time to fit residues: 78.9393 Evaluate side-chains 143 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 138 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 349 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN B 108 HIS B 720 GLN B 779 ASN A 94 GLN A 108 HIS A 720 GLN A 779 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.185319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.122223 restraints weight = 14863.748| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.27 r_work: 0.3271 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13564 Z= 0.119 Angle : 0.495 6.570 18360 Z= 0.255 Chirality : 0.040 0.157 1980 Planarity : 0.005 0.062 2282 Dihedral : 14.698 179.076 1944 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.81 % Allowed : 19.35 % Favored : 76.84 % 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: 1.82 (0.21), residues: 1562 helix: 2.46 (0.17), residues: 910 sheet: 0.22 (0.61), residues: 78 loop : -0.76 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 98 TYR 0.012 0.001 TYR B 580 PHE 0.014 0.001 PHE B 560 TRP 0.010 0.001 TRP B 829 HIS 0.003 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (13554) covalent geometry : angle 0.49433 / 0.25 (18340) SS BOND : bond 0.00095 / 0.05 ( 10) SS BOND : angle 1.05992 / 0.64 ( 20) hydrogen bonds : bond 0.03910 / 2.65 ( 734) hydrogen bonds : angle 3.96294 / 2.71 ( 2142) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 156 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 ASP cc_start: 0.7783 (t0) cc_final: 0.7489 (t0) REVERT: B 140 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7758 (tp30) REVERT: B 235 ARG cc_start: 0.8075 (ttt90) cc_final: 0.6515 (tmm160) REVERT: B 631 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7013 (mmt) REVERT: B 667 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7964 (mm-30) REVERT: B 714 MET cc_start: 0.8047 (mmm) cc_final: 0.7828 (mtp) REVERT: B 842 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.7909 (ttt) REVERT: A 60 ASP cc_start: 0.7751 (t0) cc_final: 0.7416 (t0) REVERT: A 140 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7704 (tp30) REVERT: A 235 ARG cc_start: 0.7987 (ttt90) cc_final: 0.6578 (tmm160) REVERT: A 667 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7986 (mm-30) REVERT: A 714 MET cc_start: 0.8028 (mmm) cc_final: 0.7825 (ttm) REVERT: A 842 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.7945 (ttt) outliers start: 54 outliers final: 15 residues processed: 194 average time/residue: 0.5105 time to fit residues: 109.6679 Evaluate side-chains 162 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 875 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 842 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 96 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 148 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN B 108 HIS B 632 ASN B 710 GLN B 779 ASN ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 HIS A 779 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.182241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119217 restraints weight = 14891.135| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.24 r_work: 0.3231 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13564 Z= 0.144 Angle : 0.507 6.567 18360 Z= 0.263 Chirality : 0.040 0.159 1980 Planarity : 0.005 0.069 2282 Dihedral : 13.676 171.187 1942 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.74 % Allowed : 20.20 % Favored : 76.06 % 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: 1.70 (0.21), residues: 1562 helix: 2.40 (0.17), residues: 896 sheet: 0.22 (0.62), residues: 78 loop : -0.80 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 98 TYR 0.016 0.001 TYR A 77 PHE 0.015 0.001 PHE A 393 TRP 0.011 0.001 TRP B 829 HIS 0.004 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (13554) covalent geometry : angle 0.50573 / 0.26 (18340) SS BOND : bond 0.00134 / 0.07 ( 10) SS BOND : angle 1.21216 / 0.73 ( 20) hydrogen bonds : bond 0.04193 / 2.85 ( 734) hydrogen bonds : angle 3.98121 / 2.73 ( 2142) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 154 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 ASP cc_start: 0.7840 (t0) cc_final: 0.7626 (t0) REVERT: B 140 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7876 (tp30) REVERT: B 183 PHE cc_start: 0.7140 (m-80) cc_final: 0.6934 (m-10) REVERT: B 235 ARG cc_start: 0.8113 (ttt90) cc_final: 0.6496 (tmm160) REVERT: B 360 ARG cc_start: 0.8127 (mtt90) cc_final: 0.7917 (mtt-85) REVERT: B 842 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.7973 (ttt) REVERT: A 60 ASP cc_start: 0.7864 (t0) cc_final: 0.7615 (t0) REVERT: A 140 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7802 (tp30) REVERT: A 183 PHE cc_start: 0.7066 (m-80) cc_final: 0.6855 (m-10) REVERT: A 235 ARG cc_start: 0.8056 (ttt90) cc_final: 0.6518 (tmm160) REVERT: A 534 MET cc_start: 0.7604 (tmm) cc_final: 0.7209 (tmt) REVERT: A 842 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8016 (ttt) outliers start: 53 outliers final: 12 residues processed: 185 average time/residue: 0.5332 time to fit residues: 108.5594 Evaluate side-chains 158 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 875 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 842 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 45 optimal weight: 4.9990 chunk 76 optimal weight: 0.3980 chunk 19 optimal weight: 0.0870 chunk 3 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 146 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 779 ASN A 94 GLN ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 ASN A 710 GLN A 779 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.183339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.120774 restraints weight = 14742.946| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.22 r_work: 0.3252 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13564 Z= 0.115 Angle : 0.488 6.690 18360 Z= 0.253 Chirality : 0.040 0.166 1980 Planarity : 0.005 0.070 2282 Dihedral : 12.622 160.802 1938 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.11 % Allowed : 21.12 % Favored : 75.78 % 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: 1.72 (0.21), residues: 1562 helix: 2.37 (0.17), residues: 912 sheet: 0.18 (0.63), residues: 78 loop : -0.80 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 360 TYR 0.017 0.001 TYR B 77 PHE 0.012 0.001 PHE B 560 TRP 0.010 0.001 TRP B 829 HIS 0.004 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (13554) covalent geometry : angle 0.48728 / 0.25 (18340) SS BOND : bond 0.00142 / 0.07 ( 10) SS BOND : angle 0.99929 / 0.60 ( 20) hydrogen bonds : bond 0.03872 / 2.62 ( 734) hydrogen bonds : angle 3.89270 / 2.68 ( 2142) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7891 (tp30) REVERT: B 183 PHE cc_start: 0.7192 (m-80) cc_final: 0.6934 (m-10) REVERT: B 235 ARG cc_start: 0.8030 (ttt90) cc_final: 0.6501 (tmm160) REVERT: B 360 ARG cc_start: 0.8234 (mtt90) cc_final: 0.8022 (mtt-85) REVERT: B 631 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.7029 (mmt) REVERT: B 714 MET cc_start: 0.8031 (mtm) cc_final: 0.7806 (mmm) REVERT: B 842 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7942 (ttt) REVERT: A 60 ASP cc_start: 0.7833 (t0) cc_final: 0.7607 (t0) REVERT: A 140 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7798 (tp30) REVERT: A 183 PHE cc_start: 0.7106 (m-80) cc_final: 0.6885 (m-10) REVERT: A 235 ARG cc_start: 0.7923 (ttt90) cc_final: 0.6525 (tmm160) REVERT: A 534 MET cc_start: 0.7577 (tmm) cc_final: 0.7145 (tmt) REVERT: A 714 MET cc_start: 0.8037 (mtm) cc_final: 0.7832 (mmm) REVERT: A 842 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.7985 (ttt) outliers start: 44 outliers final: 16 residues processed: 187 average time/residue: 0.5125 time to fit residues: 106.1623 Evaluate side-chains 158 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 875 THR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 842 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 18 optimal weight: 7.9990 chunk 152 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 110 optimal weight: 0.0010 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN B 779 ASN ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.181611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.118684 restraints weight = 14898.593| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.23 r_work: 0.3217 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13564 Z= 0.141 Angle : 0.512 6.845 18360 Z= 0.266 Chirality : 0.040 0.162 1980 Planarity : 0.005 0.069 2282 Dihedral : 12.380 153.092 1938 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.18 % Allowed : 21.68 % Favored : 75.14 % 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: 1.60 (0.21), residues: 1562 helix: 2.32 (0.17), residues: 908 sheet: 0.13 (0.63), residues: 78 loop : -0.90 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 360 TYR 0.022 0.001 TYR B 77 PHE 0.014 0.001 PHE B 393 TRP 0.011 0.001 TRP A 132 HIS 0.004 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (13554) covalent geometry : angle 0.51098 / 0.27 (18340) SS BOND : bond 0.00148 / 0.07 ( 10) SS BOND : angle 1.15424 / 0.69 ( 20) hydrogen bonds : bond 0.04144 / 2.81 ( 734) hydrogen bonds : angle 3.95668 / 2.73 ( 2142) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 144 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 ASP cc_start: 0.7795 (t0) cc_final: 0.7594 (t0) REVERT: B 140 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7913 (tp30) REVERT: B 183 PHE cc_start: 0.7175 (m-80) cc_final: 0.6921 (m-10) REVERT: B 235 ARG cc_start: 0.8016 (ttt90) cc_final: 0.6524 (tmm160) REVERT: B 360 ARG cc_start: 0.8227 (mtt90) cc_final: 0.7967 (mtt-85) REVERT: B 842 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.7976 (ttt) REVERT: A 60 ASP cc_start: 0.7845 (t0) cc_final: 0.7610 (t0) REVERT: A 98 ARG cc_start: 0.7253 (ttp80) cc_final: 0.6994 (ttp80) REVERT: A 140 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7914 (tp30) REVERT: A 183 PHE cc_start: 0.7168 (m-80) cc_final: 0.6867 (m-10) REVERT: A 235 ARG cc_start: 0.7924 (ttt90) cc_final: 0.6506 (tmm160) REVERT: A 534 MET cc_start: 0.7560 (tmm) cc_final: 0.7031 (tmt) REVERT: A 842 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8007 (ttt) outliers start: 45 outliers final: 19 residues processed: 171 average time/residue: 0.5446 time to fit residues: 102.8221 Evaluate side-chains 159 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 875 THR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 842 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 126 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 87 optimal weight: 0.0570 chunk 102 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 ASN ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.179023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.120869 restraints weight = 14814.392| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.42 r_work: 0.3176 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13564 Z= 0.177 Angle : 0.544 6.721 18360 Z= 0.284 Chirality : 0.042 0.166 1980 Planarity : 0.005 0.068 2282 Dihedral : 12.190 145.815 1938 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.04 % Allowed : 21.96 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.40 (0.21), residues: 1562 helix: 2.20 (0.17), residues: 898 sheet: 0.05 (0.64), residues: 78 loop : -1.02 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 360 TYR 0.021 0.001 TYR A 77 PHE 0.015 0.001 PHE B 393 TRP 0.016 0.002 TRP A 132 HIS 0.004 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (13554) covalent geometry : angle 0.54206 / 0.28 (18340) SS BOND : bond 0.00165 / 0.09 ( 10) SS BOND : angle 1.32805 / 0.80 ( 20) hydrogen bonds : bond 0.04507 / 3.06 ( 734) hydrogen bonds : angle 4.04214 / 2.79 ( 2142) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8064 (tp30) REVERT: B 183 PHE cc_start: 0.7266 (m-80) cc_final: 0.6957 (m-10) REVERT: B 235 ARG cc_start: 0.7979 (ttt90) cc_final: 0.6501 (tmm160) REVERT: B 360 ARG cc_start: 0.8309 (mtt90) cc_final: 0.8040 (mtt-85) REVERT: B 842 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8029 (ttt) REVERT: A 60 ASP cc_start: 0.7944 (t0) cc_final: 0.7672 (t0) REVERT: A 140 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8015 (tp30) REVERT: A 183 PHE cc_start: 0.7281 (m-80) cc_final: 0.6925 (m-10) REVERT: A 235 ARG cc_start: 0.8043 (ttt90) cc_final: 0.6574 (tmm160) REVERT: A 534 MET cc_start: 0.7620 (tmm) cc_final: 0.7192 (tmt) REVERT: A 842 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8063 (ttt) outliers start: 43 outliers final: 21 residues processed: 168 average time/residue: 0.5663 time to fit residues: 104.8469 Evaluate side-chains 165 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 650 TRP Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 875 THR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 650 TRP Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 842 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 1 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 112 optimal weight: 30.0000 chunk 47 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.180102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.122255 restraints weight = 14745.943| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.41 r_work: 0.3196 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13564 Z= 0.140 Angle : 0.520 7.248 18360 Z= 0.271 Chirality : 0.041 0.164 1980 Planarity : 0.005 0.068 2282 Dihedral : 11.655 132.033 1938 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.68 % Allowed : 22.88 % Favored : 74.44 % 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: 1.44 (0.21), residues: 1562 helix: 2.26 (0.17), residues: 896 sheet: -0.11 (0.63), residues: 78 loop : -1.02 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 98 TYR 0.024 0.001 TYR A 77 PHE 0.013 0.001 PHE B 560 TRP 0.018 0.002 TRP A 132 HIS 0.004 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (13554) covalent geometry : angle 0.51852 / 0.27 (18340) SS BOND : bond 0.00161 / 0.08 ( 10) SS BOND : angle 1.11806 / 0.67 ( 20) hydrogen bonds : bond 0.04190 / 2.84 ( 734) hydrogen bonds : angle 3.95604 / 2.72 ( 2142) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7564 (mt-10) REVERT: B 122 LYS cc_start: 0.7461 (mmtt) cc_final: 0.7040 (mmmt) REVERT: B 140 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8054 (tp30) REVERT: B 183 PHE cc_start: 0.7262 (m-80) cc_final: 0.6932 (m-10) REVERT: B 235 ARG cc_start: 0.7966 (ttt90) cc_final: 0.6496 (tmm160) REVERT: B 360 ARG cc_start: 0.8274 (mtt90) cc_final: 0.7992 (mtt-85) REVERT: B 842 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8009 (ttt) REVERT: A 60 ASP cc_start: 0.7955 (t0) cc_final: 0.7650 (t0) REVERT: A 98 ARG cc_start: 0.7467 (ttp80) cc_final: 0.7084 (ttp80) REVERT: A 122 LYS cc_start: 0.7776 (mmtt) cc_final: 0.7552 (mmmt) REVERT: A 140 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8020 (tp30) REVERT: A 183 PHE cc_start: 0.7267 (m-80) cc_final: 0.6908 (m-10) REVERT: A 235 ARG cc_start: 0.7999 (ttt90) cc_final: 0.6547 (tmm160) REVERT: A 534 MET cc_start: 0.7581 (tmm) cc_final: 0.7133 (tmt) REVERT: A 842 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.7990 (ttt) outliers start: 38 outliers final: 21 residues processed: 163 average time/residue: 0.5761 time to fit residues: 103.2370 Evaluate side-chains 157 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 650 TRP Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain B residue 875 THR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 650 TRP Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 842 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 16 optimal weight: 0.0980 chunk 122 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 83 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 chunk 114 optimal weight: 30.0000 chunk 29 optimal weight: 7.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN B 779 ASN ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 GLN A 779 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.184290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.122017 restraints weight = 14654.951| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.22 r_work: 0.3231 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13564 Z= 0.103 Angle : 0.493 8.030 18360 Z= 0.255 Chirality : 0.040 0.170 1980 Planarity : 0.005 0.068 2282 Dihedral : 10.609 100.301 1938 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.33 % Allowed : 23.52 % Favored : 74.15 % 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: 1.61 (0.21), residues: 1562 helix: 2.36 (0.17), residues: 912 sheet: -0.20 (0.63), residues: 78 loop : -0.94 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 98 TYR 0.022 0.001 TYR A 77 PHE 0.012 0.001 PHE A 560 TRP 0.021 0.002 TRP A 132 HIS 0.003 0.000 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (13554) covalent geometry : angle 0.49280 / 0.25 (18340) SS BOND : bond 0.00154 / 0.07 ( 10) SS BOND : angle 0.82260 / 0.49 ( 20) hydrogen bonds : bond 0.03676 / 2.49 ( 734) hydrogen bonds : angle 3.80875 / 2.62 ( 2142) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 LYS cc_start: 0.7474 (mmtt) cc_final: 0.7058 (mmmt) REVERT: B 140 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7891 (tp30) REVERT: B 183 PHE cc_start: 0.7235 (m-80) cc_final: 0.6949 (m-10) REVERT: B 235 ARG cc_start: 0.7917 (ttt90) cc_final: 0.6455 (tmm160) REVERT: B 779 ASN cc_start: 0.7772 (m-40) cc_final: 0.7544 (m-40) REVERT: B 842 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.7969 (ttt) REVERT: A 60 ASP cc_start: 0.7925 (t0) cc_final: 0.7672 (t0) REVERT: A 98 ARG cc_start: 0.7346 (ttp80) cc_final: 0.7067 (ttp80) REVERT: A 122 LYS cc_start: 0.7811 (mmtt) cc_final: 0.7571 (mmmt) REVERT: A 140 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7913 (tp30) REVERT: A 183 PHE cc_start: 0.7210 (m-80) cc_final: 0.6878 (m-10) REVERT: A 235 ARG cc_start: 0.7921 (ttt90) cc_final: 0.6535 (tmm160) REVERT: A 534 MET cc_start: 0.7585 (tmm) cc_final: 0.7128 (tmt) REVERT: A 714 MET cc_start: 0.8050 (mmm) cc_final: 0.7838 (mtm) REVERT: A 842 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7964 (ttt) outliers start: 33 outliers final: 18 residues processed: 171 average time/residue: 0.5340 time to fit residues: 100.6499 Evaluate side-chains 159 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 650 TRP Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 875 THR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 650 TRP Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 842 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 121 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 88 optimal weight: 0.4980 chunk 134 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 HIS A 779 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.183432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.120822 restraints weight = 14793.465| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.22 r_work: 0.3248 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13564 Z= 0.117 Angle : 0.511 8.157 18360 Z= 0.264 Chirality : 0.040 0.181 1980 Planarity : 0.005 0.068 2282 Dihedral : 10.416 89.373 1938 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.19 % Allowed : 24.01 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.21), residues: 1562 helix: 2.34 (0.17), residues: 908 sheet: -0.22 (0.63), residues: 78 loop : -0.97 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 98 TYR 0.029 0.001 TYR B 77 PHE 0.014 0.001 PHE B 560 TRP 0.021 0.001 TRP A 132 HIS 0.003 0.000 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (13554) covalent geometry : angle 0.51001 / 0.26 (18340) SS BOND : bond 0.00144 / 0.07 ( 10) SS BOND : angle 0.95550 / 0.57 ( 20) hydrogen bonds : bond 0.03804 / 2.58 ( 734) hydrogen bonds : angle 3.82809 / 2.62 ( 2142) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 LYS cc_start: 0.7493 (mmtt) cc_final: 0.7084 (mmmt) REVERT: B 140 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7870 (tp30) REVERT: B 183 PHE cc_start: 0.7247 (m-80) cc_final: 0.6916 (m-10) REVERT: B 235 ARG cc_start: 0.7898 (ttt90) cc_final: 0.6435 (tmm160) REVERT: B 842 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.7977 (ttt) REVERT: A 60 ASP cc_start: 0.7950 (t0) cc_final: 0.7696 (t0) REVERT: A 98 ARG cc_start: 0.7413 (ttp80) cc_final: 0.7056 (ttp80) REVERT: A 122 LYS cc_start: 0.7803 (mmtt) cc_final: 0.7571 (mmmt) REVERT: A 140 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7937 (tp30) REVERT: A 183 PHE cc_start: 0.7222 (m-80) cc_final: 0.6887 (m-10) REVERT: A 235 ARG cc_start: 0.7945 (ttt90) cc_final: 0.6547 (tmm160) REVERT: A 534 MET cc_start: 0.7546 (tmm) cc_final: 0.7079 (tmt) REVERT: A 842 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.7970 (ttt) outliers start: 31 outliers final: 20 residues processed: 164 average time/residue: 0.5505 time to fit residues: 99.6982 Evaluate side-chains 161 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 650 TRP Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 875 THR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 650 TRP Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 866 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 102 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 34 optimal weight: 30.0000 chunk 60 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 105 optimal weight: 0.0370 chunk 63 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 overall best weight: 0.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 ASN A 559 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.183381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120901 restraints weight = 14831.368| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.23 r_work: 0.3239 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13564 Z= 0.118 Angle : 0.510 8.301 18360 Z= 0.264 Chirality : 0.040 0.186 1980 Planarity : 0.005 0.069 2282 Dihedral : 10.055 86.298 1938 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.84 % Allowed : 24.01 % Favored : 74.15 % 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: 1.55 (0.21), residues: 1562 helix: 2.33 (0.17), residues: 908 sheet: -0.31 (0.62), residues: 78 loop : -0.97 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 360 TYR 0.045 0.001 TYR B 77 PHE 0.013 0.001 PHE A 560 TRP 0.021 0.002 TRP A 132 HIS 0.003 0.000 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (13554) covalent geometry : angle 0.50979 / 0.26 (18340) SS BOND : bond 0.00141 / 0.07 ( 10) SS BOND : angle 0.95199 / 0.57 ( 20) hydrogen bonds : bond 0.03841 / 2.61 ( 734) hydrogen bonds : angle 3.87186 / 2.66 ( 2142) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 LYS cc_start: 0.7599 (mmtt) cc_final: 0.7191 (mmmt) REVERT: B 140 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7877 (tp30) REVERT: B 183 PHE cc_start: 0.7235 (m-80) cc_final: 0.6900 (m-10) REVERT: B 235 ARG cc_start: 0.7913 (ttt90) cc_final: 0.6472 (tmm160) REVERT: B 714 MET cc_start: 0.8050 (mmm) cc_final: 0.7781 (mtm) REVERT: B 842 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7967 (ttt) REVERT: A 60 ASP cc_start: 0.7950 (t0) cc_final: 0.7681 (t0) REVERT: A 122 LYS cc_start: 0.7840 (mmtt) cc_final: 0.7593 (mmmt) REVERT: A 140 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7918 (tp30) REVERT: A 183 PHE cc_start: 0.7215 (m-80) cc_final: 0.6856 (m-10) REVERT: A 235 ARG cc_start: 0.7936 (ttt90) cc_final: 0.6546 (tmm160) REVERT: A 534 MET cc_start: 0.7544 (tmm) cc_final: 0.7070 (tmt) REVERT: A 842 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7970 (ttt) outliers start: 26 outliers final: 18 residues processed: 162 average time/residue: 0.5685 time to fit residues: 101.5115 Evaluate side-chains 160 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 650 TRP Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 875 THR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 650 TRP Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 866 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 67 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 66 optimal weight: 0.0980 chunk 133 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN A 559 GLN A 779 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.181912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.119148 restraints weight = 14726.372| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.22 r_work: 0.3210 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13564 Z= 0.136 Angle : 0.525 8.257 18360 Z= 0.273 Chirality : 0.041 0.188 1980 Planarity : 0.005 0.068 2282 Dihedral : 9.978 88.500 1938 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.91 % Allowed : 24.08 % Favored : 74.01 % 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: 1.47 (0.21), residues: 1562 helix: 2.28 (0.17), residues: 908 sheet: -0.40 (0.61), residues: 78 loop : -1.02 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 98 TYR 0.045 0.001 TYR A 77 PHE 0.013 0.001 PHE A 560 TRP 0.020 0.001 TRP A 132 HIS 0.004 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (13554) covalent geometry : angle 0.52447 / 0.27 (18340) SS BOND : bond 0.00151 / 0.08 ( 10) SS BOND : angle 1.07252 / 0.65 ( 20) hydrogen bonds : bond 0.04056 / 2.76 ( 734) hydrogen bonds : angle 3.91821 / 2.69 ( 2142) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4822.87 seconds wall clock time: 82 minutes 48.46 seconds (4968.46 seconds total)