Starting phenix.real_space_refine on Fri Jul 3 09:51:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o1o_70014/07_2026/9o1o_70014.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o1o_70014/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9o1o_70014/07_2026/9o1o_70014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o1o_70014/07_2026/9o1o_70014.map" model { file = "/net/cci-nas-00/data/ceres_data/9o1o_70014/07_2026/9o1o_70014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o1o_70014/07_2026/9o1o_70014.cif" } 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-6108/lib/python3.11/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, 111 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'PGW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 3 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: 5.30, per 1000 atoms: 0.40 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 435.0 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: 0.24 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: 2.06 Time building geometry restraints manager: 1.34 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 3.250 ... (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: 0.03 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: 0.980 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.450 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:5.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 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 : 0.426 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: 0.3995 time to fit residues: 71.3171 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 : 0.492 ------------------------------------------------------------------------------- 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: 2.9990 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... 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 = 0.4108 r_free = 0.4108 target = 0.185391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.123116 restraints weight = 14865.091| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.24 r_work: 0.3290 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.0833 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= 0.121 Angle : 0.495 6.558 18360 Z= 0.256 Chirality : 0.040 0.157 1980 Planarity : 0.005 0.062 2282 Dihedral : 14.755 179.912 1944 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.74 % Allowed : 19.49 % Favored : 76.77 % 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: 1.83 (0.21), residues: 1562 helix: 2.47 (0.17), residues: 910 sheet: 0.21 (0.61), residues: 78 loop : -0.76 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 98 TYR 0.012 0.001 TYR B 580 PHE 0.014 0.001 PHE B 560 TRP 0.011 0.001 TRP B 829 HIS 0.003 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (13554) covalent geometry : angle 0.49445 / 0.26 (18340) SS BOND : bond 0.00101 / 0.05 ( 10) SS BOND : angle 1.06750 / 0.64 ( 20) hydrogen bonds : bond 0.03901 / 2.65 ( 734) hydrogen bonds : angle 3.98027 / 2.72 ( 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 209 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 156 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 ASP cc_start: 0.7776 (t0) cc_final: 0.7482 (t0) REVERT: B 140 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7759 (tp30) REVERT: B 235 ARG cc_start: 0.8084 (ttt90) cc_final: 0.6516 (tmm160) REVERT: B 631 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7017 (mmt) REVERT: B 667 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7607 (mm-30) REVERT: B 714 MET cc_start: 0.8062 (mmm) cc_final: 0.7846 (mtp) REVERT: B 842 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.7927 (ttt) REVERT: A 60 ASP cc_start: 0.7725 (t0) cc_final: 0.7380 (t0) REVERT: A 140 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7703 (tp30) REVERT: A 235 ARG cc_start: 0.7991 (ttt90) cc_final: 0.6580 (tmm160) REVERT: A 667 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7645 (mm-30) REVERT: A 842 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.7966 (ttt) outliers start: 53 outliers final: 15 residues processed: 193 average time/residue: 0.4869 time to fit residues: 104.5295 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 : 0.463 ------------------------------------------------------------------------------- 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: 9.9990 chunk 50 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 148 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 ASN B 108 HIS 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.178815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.115667 restraints weight = 14917.473| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.27 r_work: 0.3165 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13564 Z= 0.199 Angle : 0.560 6.424 18360 Z= 0.292 Chirality : 0.042 0.159 1980 Planarity : 0.005 0.070 2282 Dihedral : 14.227 176.133 1942 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.17 % Allowed : 20.55 % Favored : 75.28 % 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: 1.43 (0.21), residues: 1562 helix: 2.20 (0.17), residues: 896 sheet: 0.14 (0.62), residues: 78 loop : -0.97 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 98 TYR 0.018 0.002 TYR B 222 PHE 0.017 0.002 PHE B 393 TRP 0.011 0.001 TRP A 829 HIS 0.005 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 (13554) covalent geometry : angle 0.55847 / 0.29 (18340) SS BOND : bond 0.00180 / 0.09 ( 10) SS BOND : angle 1.47277 / 0.89 ( 20) hydrogen bonds : bond 0.04734 / 3.23 ( 734) hydrogen bonds : angle 4.14350 / 2.85 ( 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 216 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 157 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 ASP cc_start: 0.7937 (t0) cc_final: 0.7697 (t0) REVERT: B 140 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7996 (tp30) REVERT: B 183 PHE cc_start: 0.7098 (m-80) cc_final: 0.6860 (m-10) REVERT: B 235 ARG cc_start: 0.8081 (ttt90) cc_final: 0.6457 (tmm160) REVERT: B 360 ARG cc_start: 0.8122 (mtt90) cc_final: 0.7908 (mtt-85) REVERT: B 714 MET cc_start: 0.8146 (mmm) cc_final: 0.7918 (mtm) REVERT: B 774 ASP cc_start: 0.9100 (m-30) cc_final: 0.8832 (m-30) REVERT: B 842 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.7986 (ttt) REVERT: A 60 ASP cc_start: 0.7940 (t0) cc_final: 0.7694 (t0) REVERT: A 73 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8759 (t80) REVERT: A 122 LYS cc_start: 0.7535 (mmtt) cc_final: 0.7333 (mmmt) REVERT: A 132 TRP cc_start: 0.7111 (t-100) cc_final: 0.6888 (t-100) REVERT: A 140 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7933 (tp30) REVERT: A 183 PHE cc_start: 0.7079 (m-80) cc_final: 0.6779 (m-10) REVERT: A 235 ARG cc_start: 0.8087 (ttt90) cc_final: 0.6524 (tmm160) REVERT: A 534 MET cc_start: 0.7544 (tmm) cc_final: 0.7191 (tmt) REVERT: A 774 ASP cc_start: 0.9101 (m-30) cc_final: 0.8837 (m-30) REVERT: A 842 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.7961 (ttt) outliers start: 59 outliers final: 17 residues processed: 186 average time/residue: 0.4802 time to fit residues: 98.4848 Evaluate side-chains 168 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 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 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 73 PHE 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 349 CYS Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 650 TRP Chi-restraints excluded: chain A residue 659 MET 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: 2.9990 chunk 76 optimal weight: 0.8980 chunk 19 optimal weight: 0.0170 chunk 3 optimal weight: 10.0000 chunk 125 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 142 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 94 GLN B 559 GLN B 632 ASN B 710 GLN B 779 ASN ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 GLN A 632 ASN A 710 GLN A 779 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.183511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.126205 restraints weight = 14768.676| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.40 r_work: 0.3264 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13564 Z= 0.104 Angle : 0.484 6.867 18360 Z= 0.252 Chirality : 0.039 0.168 1980 Planarity : 0.005 0.069 2282 Dihedral : 12.548 158.334 1938 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.97 % Allowed : 21.96 % Favored : 75.07 % 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: 1.67 (0.21), residues: 1562 helix: 2.37 (0.17), residues: 910 sheet: 0.15 (0.63), residues: 78 loop : -0.88 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 360 TYR 0.019 0.001 TYR A 855 PHE 0.012 0.001 PHE B 560 TRP 0.011 0.001 TRP B 273 HIS 0.003 0.000 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (13554) covalent geometry : angle 0.48345 / 0.25 (18340) SS BOND : bond 0.00159 / 0.08 ( 10) SS BOND : angle 0.89769 / 0.54 ( 20) hydrogen bonds : bond 0.03785 / 2.57 ( 734) hydrogen bonds : angle 3.90761 / 2.69 ( 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: 42 poor density : 159 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7951 (tp30) REVERT: B 183 PHE cc_start: 0.7120 (m-80) cc_final: 0.6889 (m-10) REVERT: B 235 ARG cc_start: 0.7982 (ttt90) cc_final: 0.6539 (tmm160) REVERT: B 360 ARG cc_start: 0.8219 (mtt90) cc_final: 0.7977 (mtt-85) REVERT: B 631 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6945 (mmt) REVERT: B 667 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7595 (mm-30) REVERT: B 842 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.7978 (ttt) REVERT: A 60 ASP cc_start: 0.7828 (t0) cc_final: 0.7601 (t0) REVERT: A 132 TRP cc_start: 0.7169 (t-100) cc_final: 0.6870 (t-100) REVERT: A 140 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7905 (tp30) REVERT: A 183 PHE cc_start: 0.7072 (m-80) cc_final: 0.6837 (m-10) REVERT: A 235 ARG cc_start: 0.8064 (ttt90) cc_final: 0.6509 (tmm160) REVERT: A 534 MET cc_start: 0.7553 (tmm) cc_final: 0.7043 (tmt) REVERT: A 667 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7605 (mm-30) REVERT: A 842 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.7946 (ttt) outliers start: 42 outliers final: 12 residues processed: 185 average time/residue: 0.4704 time to fit residues: 96.5291 Evaluate side-chains 156 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 242 TYR Chi-restraints excluded: chain B residue 349 CYS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 18 optimal weight: 7.9990 chunk 152 optimal weight: 0.0870 chunk 77 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 110 optimal weight: 0.1980 chunk 112 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 118 optimal weight: 8.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 559 GLN B 779 ASN A 94 GLN A 559 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 = 0.4075 r_free = 0.4075 target = 0.182364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120340 restraints weight = 14867.698| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.21 r_work: 0.3232 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1564 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= 0.123 Angle : 0.501 6.968 18360 Z= 0.260 Chirality : 0.040 0.162 1980 Planarity : 0.005 0.068 2282 Dihedral : 12.126 148.102 1938 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.25 % Allowed : 22.03 % Favored : 74.72 % 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: 1.62 (0.21), residues: 1562 helix: 2.34 (0.17), residues: 908 sheet: 0.10 (0.63), residues: 78 loop : -0.92 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 98 TYR 0.024 0.001 TYR A 77 PHE 0.013 0.001 PHE A 560 TRP 0.011 0.001 TRP B 132 HIS 0.003 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (13554) covalent geometry : angle 0.49970 / 0.26 (18340) SS BOND : bond 0.00149 / 0.07 ( 10) SS BOND : angle 1.04457 / 0.63 ( 20) hydrogen bonds : bond 0.03933 / 2.67 ( 734) hydrogen bonds : angle 3.92274 / 2.70 ( 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 194 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 ASP cc_start: 0.7737 (t0) cc_final: 0.7496 (t0) REVERT: B 140 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7897 (tp30) REVERT: B 183 PHE cc_start: 0.7121 (m-80) cc_final: 0.6894 (m-10) REVERT: B 235 ARG cc_start: 0.7955 (ttt90) cc_final: 0.6488 (tmm160) REVERT: B 360 ARG cc_start: 0.8212 (mtt90) cc_final: 0.7952 (mtt-85) REVERT: B 631 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.6943 (mmt) REVERT: B 667 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7680 (mm-30) REVERT: B 842 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.7958 (ttt) REVERT: A 60 ASP cc_start: 0.7803 (t0) cc_final: 0.7582 (t0) REVERT: A 132 TRP cc_start: 0.7183 (t-100) cc_final: 0.6860 (t-100) REVERT: A 140 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7931 (tp30) REVERT: A 183 PHE cc_start: 0.7137 (m-80) cc_final: 0.6884 (m-10) REVERT: A 235 ARG cc_start: 0.7950 (ttt90) cc_final: 0.6563 (tmm160) REVERT: A 534 MET cc_start: 0.7551 (tmm) cc_final: 0.7020 (tmt) REVERT: A 667 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7703 (mm-30) REVERT: A 842 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.7976 (ttt) outliers start: 46 outliers final: 21 residues processed: 176 average time/residue: 0.5319 time to fit residues: 103.9263 Evaluate side-chains 168 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 530 LYS Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 620 ASN 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 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 620 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 126 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 25 optimal weight: 0.2980 chunk 103 optimal weight: 0.2980 chunk 87 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 ASN ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 ASN A 779 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.181132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.123497 restraints weight = 14818.977| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.53 r_work: 0.3214 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1699 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= 0.138 Angle : 0.513 6.953 18360 Z= 0.267 Chirality : 0.040 0.160 1980 Planarity : 0.005 0.068 2282 Dihedral : 11.619 134.233 1938 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.95 % Allowed : 21.12 % Favored : 74.93 % 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: 1.53 (0.21), residues: 1562 helix: 2.29 (0.17), residues: 908 sheet: 0.09 (0.63), residues: 78 loop : -0.98 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 360 TYR 0.022 0.001 TYR B 77 PHE 0.013 0.001 PHE B 560 TRP 0.014 0.001 TRP B 132 HIS 0.004 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (13554) covalent geometry : angle 0.51232 / 0.27 (18340) SS BOND : bond 0.00156 / 0.08 ( 10) SS BOND : angle 1.13639 / 0.68 ( 20) hydrogen bonds : bond 0.04105 / 2.79 ( 734) hydrogen bonds : angle 3.93625 / 2.71 ( 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 202 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 146 time to evaluate : 0.544 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: 0.8233 (OUTLIER) cc_final: 0.7950 (tp30) REVERT: B 183 PHE cc_start: 0.7184 (m-80) cc_final: 0.6895 (m-10) REVERT: B 235 ARG cc_start: 0.7980 (ttt90) cc_final: 0.6551 (tmm160) REVERT: B 360 ARG cc_start: 0.8234 (mtt90) cc_final: 0.7977 (mtt-85) REVERT: B 842 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8000 (ttt) REVERT: A 60 ASP cc_start: 0.7897 (t0) cc_final: 0.7643 (t0) REVERT: A 122 LYS cc_start: 0.7518 (mmtt) cc_final: 0.7266 (mmmt) REVERT: A 132 TRP cc_start: 0.7229 (t-100) cc_final: 0.6886 (t-100) REVERT: A 140 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7937 (tp30) REVERT: A 183 PHE cc_start: 0.7184 (m-80) cc_final: 0.6870 (m-10) REVERT: A 235 ARG cc_start: 0.7997 (ttt90) cc_final: 0.6566 (tmm160) REVERT: A 534 MET cc_start: 0.7516 (tmm) cc_final: 0.7020 (tmt) REVERT: A 659 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7017 (tpt) REVERT: A 842 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8020 (ttt) outliers start: 56 outliers final: 24 residues processed: 178 average time/residue: 0.5442 time to fit residues: 106.6802 Evaluate side-chains 169 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 620 ASN 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 349 CYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 650 TRP Chi-restraints excluded: chain A residue 659 MET 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: 6.9990 chunk 153 optimal weight: 0.4980 chunk 89 optimal weight: 0.0570 chunk 68 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 112 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.184164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.122265 restraints weight = 14763.637| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.22 r_work: 0.3276 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13564 Z= 0.103 Angle : 0.490 7.630 18360 Z= 0.254 Chirality : 0.040 0.163 1980 Planarity : 0.005 0.068 2282 Dihedral : 10.683 108.924 1938 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.12 % Allowed : 23.38 % Favored : 74.51 % 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: 2.41 (0.17), residues: 912 sheet: 0.06 (0.63), residues: 78 loop : -0.90 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 98 TYR 0.021 0.001 TYR A 77 PHE 0.012 0.001 PHE B 560 TRP 0.016 0.001 TRP B 132 HIS 0.003 0.000 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (13554) covalent geometry : angle 0.48993 / 0.25 (18340) SS BOND : bond 0.00146 / 0.07 ( 10) SS BOND : angle 0.86122 / 0.51 ( 20) hydrogen bonds : bond 0.03672 / 2.49 ( 734) hydrogen bonds : angle 3.82692 / 2.64 ( 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 181 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 ARG cc_start: 0.7503 (ttp80) cc_final: 0.7203 (ttp80) REVERT: B 122 LYS cc_start: 0.7490 (mmtt) cc_final: 0.7086 (mmmt) REVERT: B 140 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7881 (tp30) REVERT: B 183 PHE cc_start: 0.7184 (m-80) cc_final: 0.6880 (m-10) REVERT: B 235 ARG cc_start: 0.7872 (ttt90) cc_final: 0.6447 (tmm160) REVERT: B 272 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8126 (mp0) REVERT: B 631 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.7052 (mmt) REVERT: B 842 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7956 (ttt) REVERT: A 60 ASP cc_start: 0.7880 (t0) cc_final: 0.7618 (t0) REVERT: A 98 ARG cc_start: 0.7312 (ttp80) cc_final: 0.7031 (ttp80) REVERT: A 132 TRP cc_start: 0.7197 (t-100) cc_final: 0.6817 (t-100) REVERT: A 140 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7902 (tp30) REVERT: A 183 PHE cc_start: 0.7145 (m-80) cc_final: 0.6888 (m-10) REVERT: A 235 ARG cc_start: 0.7915 (ttt90) cc_final: 0.6480 (tmm160) REVERT: A 272 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8126 (mp0) REVERT: A 534 MET cc_start: 0.7510 (tmm) cc_final: 0.6976 (tmt) REVERT: A 842 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.7963 (ttt) outliers start: 30 outliers final: 17 residues processed: 170 average time/residue: 0.4975 time to fit residues: 93.3679 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 : 0.389 ------------------------------------------------------------------------------- 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 595 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 16 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN B 779 ASN ** A 129 HIS ** 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 = 0.4076 r_free = 0.4076 target = 0.182413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.120122 restraints weight = 14687.557| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.20 r_work: 0.3251 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13564 Z= 0.127 Angle : 0.516 7.823 18360 Z= 0.267 Chirality : 0.040 0.177 1980 Planarity : 0.005 0.068 2282 Dihedral : 10.562 88.480 1938 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.26 % Allowed : 23.80 % Favored : 73.94 % 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: 1.63 (0.21), residues: 1562 helix: 2.38 (0.17), residues: 908 sheet: 0.05 (0.63), residues: 78 loop : -0.96 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 98 TYR 0.024 0.001 TYR B 77 PHE 0.013 0.001 PHE A 393 TRP 0.018 0.001 TRP B 132 HIS 0.003 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (13554) covalent geometry : angle 0.51540 / 0.27 (18340) SS BOND : bond 0.00141 / 0.07 ( 10) SS BOND : angle 1.06235 / 0.64 ( 20) hydrogen bonds : bond 0.03937 / 2.67 ( 734) hydrogen bonds : angle 3.87135 / 2.66 ( 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 179 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 ARG cc_start: 0.7553 (ttp80) cc_final: 0.7169 (ttp80) REVERT: B 122 LYS cc_start: 0.7504 (mmtt) cc_final: 0.7103 (mmmt) REVERT: B 140 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7893 (tp30) REVERT: B 183 PHE cc_start: 0.7212 (m-80) cc_final: 0.6910 (m-10) REVERT: B 235 ARG cc_start: 0.7940 (ttt90) cc_final: 0.6502 (tmm160) REVERT: B 360 ARG cc_start: 0.8015 (mtt90) cc_final: 0.7714 (mtt-85) REVERT: B 842 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.7976 (ttt) REVERT: A 60 ASP cc_start: 0.7906 (t0) cc_final: 0.7651 (t0) REVERT: A 98 ARG cc_start: 0.7382 (ttp80) cc_final: 0.7133 (ttp80) REVERT: A 132 TRP cc_start: 0.7254 (t-100) cc_final: 0.6881 (t-100) REVERT: A 140 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7937 (tp30) REVERT: A 183 PHE cc_start: 0.7204 (m-80) cc_final: 0.6903 (m-10) REVERT: A 235 ARG cc_start: 0.7956 (ttt90) cc_final: 0.6485 (tmm160) REVERT: A 534 MET cc_start: 0.7577 (tmm) cc_final: 0.7112 (tmt) REVERT: A 842 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8000 (ttt) outliers start: 32 outliers final: 20 residues processed: 166 average time/residue: 0.5185 time to fit residues: 95.5882 Evaluate side-chains 162 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 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 349 CYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 595 GLU 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: 6.9990 chunk 75 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 114 optimal weight: 20.0000 chunk 88 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.180161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.122904 restraints weight = 14884.173| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.42 r_work: 0.3196 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13564 Z= 0.163 Angle : 0.549 7.905 18360 Z= 0.285 Chirality : 0.041 0.180 1980 Planarity : 0.005 0.067 2282 Dihedral : 10.630 88.375 1938 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.47 % Allowed : 23.73 % 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: 1.46 (0.21), residues: 1562 helix: 2.27 (0.17), residues: 898 sheet: -0.02 (0.63), residues: 78 loop : -1.01 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 98 TYR 0.039 0.001 TYR B 77 PHE 0.015 0.001 PHE A 393 TRP 0.021 0.001 TRP B 132 HIS 0.004 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 (13554) covalent geometry : angle 0.54728 / 0.28 (18340) SS BOND : bond 0.00173 / 0.09 ( 10) SS BOND : angle 1.25469 / 0.76 ( 20) hydrogen bonds : bond 0.04338 / 2.96 ( 734) hydrogen bonds : angle 3.99533 / 2.74 ( 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 179 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.454 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: 0.8302 (OUTLIER) cc_final: 0.8001 (tp30) REVERT: B 183 PHE cc_start: 0.7242 (m-80) cc_final: 0.6933 (m-10) REVERT: B 235 ARG cc_start: 0.7967 (ttt90) cc_final: 0.6516 (tmm160) REVERT: B 360 ARG cc_start: 0.8080 (mtt90) cc_final: 0.7765 (mtt-85) REVERT: B 714 MET cc_start: 0.8111 (mmm) cc_final: 0.7894 (mtm) REVERT: B 842 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8031 (ttt) REVERT: A 60 ASP cc_start: 0.7939 (t0) cc_final: 0.7652 (t0) REVERT: A 98 ARG cc_start: 0.7456 (ttp80) cc_final: 0.7199 (ttp80) REVERT: A 122 LYS cc_start: 0.7701 (mmtt) cc_final: 0.7399 (mmmt) REVERT: A 132 TRP cc_start: 0.7305 (t-100) cc_final: 0.6903 (t-100) REVERT: A 140 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8088 (tp30) REVERT: A 183 PHE cc_start: 0.7290 (m-80) cc_final: 0.6881 (m-10) REVERT: A 235 ARG cc_start: 0.8017 (ttt90) cc_final: 0.6538 (tmm160) REVERT: A 534 MET cc_start: 0.7625 (tmm) cc_final: 0.7147 (tmt) REVERT: A 714 MET cc_start: 0.8129 (mmm) cc_final: 0.7803 (mtm) REVERT: A 842 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8046 (ttt) outliers start: 35 outliers final: 22 residues processed: 162 average time/residue: 0.4765 time to fit residues: 85.8297 Evaluate side-chains 166 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 365 CYS Chi-restraints excluded: chain B residue 620 ASN 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 349 CYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 620 ASN 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=1.00 ------------------------------------------------------------------------------- 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: 4.9990 chunk 34 optimal weight: 20.0000 chunk 60 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4069 r_free = 0.4069 target = 0.181761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119488 restraints weight = 14829.682| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.21 r_work: 0.3215 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13564 Z= 0.124 Angle : 0.527 8.337 18360 Z= 0.274 Chirality : 0.040 0.182 1980 Planarity : 0.005 0.067 2282 Dihedral : 10.354 89.276 1938 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.05 % Allowed : 24.29 % Favored : 73.66 % 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: 1.54 (0.21), residues: 1562 helix: 2.33 (0.17), residues: 908 sheet: -0.12 (0.63), residues: 78 loop : -1.02 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 98 TYR 0.052 0.001 TYR A 77 PHE 0.012 0.001 PHE A 560 TRP 0.021 0.001 TRP B 132 HIS 0.003 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (13554) covalent geometry : angle 0.52659 / 0.27 (18340) SS BOND : bond 0.00156 / 0.08 ( 10) SS BOND : angle 1.01479 / 0.61 ( 20) hydrogen bonds : bond 0.04011 / 2.73 ( 734) hydrogen bonds : angle 3.94262 / 2.71 ( 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 171 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 LYS cc_start: 0.7564 (mmtt) cc_final: 0.7158 (mmmt) REVERT: B 140 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7931 (tp30) REVERT: B 183 PHE cc_start: 0.7226 (m-80) cc_final: 0.6928 (m-10) REVERT: B 235 ARG cc_start: 0.7952 (ttt90) cc_final: 0.6505 (tmm160) REVERT: B 360 ARG cc_start: 0.8021 (mtt90) cc_final: 0.7697 (mtt-85) REVERT: B 842 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.7953 (ttt) REVERT: A 60 ASP cc_start: 0.7944 (t0) cc_final: 0.7701 (t0) REVERT: A 79 ASP cc_start: 0.7668 (p0) cc_final: 0.7427 (p0) REVERT: A 98 ARG cc_start: 0.7430 (ttp80) cc_final: 0.7120 (ttp80) REVERT: A 122 LYS cc_start: 0.7706 (mmtt) cc_final: 0.7196 (mmmt) REVERT: A 132 TRP cc_start: 0.7283 (t-100) cc_final: 0.6883 (t-100) REVERT: A 140 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7990 (tp30) REVERT: A 183 PHE cc_start: 0.7232 (m-80) cc_final: 0.6836 (m-10) REVERT: A 235 ARG cc_start: 0.7984 (ttt90) cc_final: 0.6514 (tmm160) REVERT: A 534 MET cc_start: 0.7581 (tmm) cc_final: 0.7078 (tmt) REVERT: A 714 MET cc_start: 0.8075 (mmm) cc_final: 0.7806 (mtm) REVERT: A 842 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.7998 (ttt) outliers start: 29 outliers final: 20 residues processed: 158 average time/residue: 0.5480 time to fit residues: 95.5510 Evaluate side-chains 164 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 365 CYS 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 349 CYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 595 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 67 optimal weight: 3.9990 chunk 87 optimal weight: 0.0970 chunk 98 optimal weight: 0.0770 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 133 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 779 ASN ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 HIS A 308 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.185435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.124818 restraints weight = 14738.154| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.18 r_work: 0.3280 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13564 Z= 0.103 Angle : 0.504 8.473 18360 Z= 0.260 Chirality : 0.040 0.184 1980 Planarity : 0.005 0.069 2282 Dihedral : 9.547 87.432 1938 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.48 % Allowed : 24.93 % Favored : 73.59 % 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: 2.47 (0.17), residues: 910 sheet: -0.18 (0.62), residues: 78 loop : -0.97 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 98 TYR 0.043 0.001 TYR A 77 PHE 0.012 0.001 PHE A 560 TRP 0.018 0.001 TRP B 132 HIS 0.003 0.000 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (13554) covalent geometry : angle 0.50337 / 0.26 (18340) SS BOND : bond 0.00132 / 0.06 ( 10) SS BOND : angle 0.78811 / 0.47 ( 20) hydrogen bonds : bond 0.03555 / 2.41 ( 734) hydrogen bonds : angle 3.80385 / 2.62 ( 2142) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4416.45 seconds wall clock time: 76 minutes 2.53 seconds (4562.53 seconds total)