Starting phenix.real_space_refine on Sun May 3 16:08:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o1i_70008/05_2026/9o1i_70008.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o1i_70008/05_2026/9o1i_70008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o1i_70008/05_2026/9o1i_70008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o1i_70008/05_2026/9o1i_70008.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o1i_70008/05_2026/9o1i_70008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o1i_70008/05_2026/9o1i_70008.map" } resolution = 2.49 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= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 82 5.16 5 C 9248 2.51 5 N 2224 2.21 5 O 2524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14090 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 6840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6840 Classifications: {'peptide': 830} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 38, 'TRANS': 791} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 205 Unusual residues: {'PGW': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 11 Restraints were copied for chains: A Time building chain proxies: 6.74, per 1000 atoms: 0.48 Number of scatterers: 14090 At special positions: 0 Unit cell: (136.125, 98.175, 117.975, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 12 15.00 O 2524 8.00 N 2224 7.00 C 9248 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: 1.13 Conformation dependent library (CDL) restraints added in 511.9 milliseconds 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3168 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 12 sheets defined 58.4% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'B' and resid 90 through 108 Processing helix chain 'B' and resid 131 through 142 removed outlier: 3.548A pdb=" N MET B 142 " --> pdb=" O TYR B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 157 removed outlier: 3.543A pdb=" N SER B 157 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 195 removed outlier: 4.096A pdb=" N MET B 192 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ASN B 193 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP B 194 " --> pdb=" O ARG B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 218 Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 293 through 327 removed outlier: 3.522A pdb=" N TYR B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 339 removed outlier: 3.521A pdb=" N LYS B 335 " --> pdb=" O CYS B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.043A pdb=" N LYS B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 409 removed outlier: 3.667A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 426 removed outlier: 3.941A pdb=" N GLN B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 487 removed outlier: 3.616A pdb=" N CYS B 456 " --> pdb=" O ARG B 452 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ALA B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 477 " --> pdb=" O GLY B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 509 removed outlier: 3.694A pdb=" N THR B 509 " --> pdb=" O PRO B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 539 removed outlier: 3.583A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 574 removed outlier: 5.417A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 625 Processing helix chain 'B' and resid 625 through 638 Processing helix chain 'B' and resid 648 through 655 removed outlier: 3.645A pdb=" N HIS B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 680 Processing helix chain 'B' and resid 687 through 710 removed outlier: 3.548A pdb=" N LEU B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 removed outlier: 4.107A pdb=" N ILE B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.020A 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 775 through 781 Processing helix chain 'B' and resid 787 through 789 No H-bonds generated for 'chain 'B' and resid 787 through 789' Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 886 removed outlier: 3.740A pdb=" N LEU B 879 " --> pdb=" O THR B 875 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP B 886 " --> pdb=" O SER B 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 108 Processing helix chain 'A' and resid 131 through 142 removed outlier: 3.548A pdb=" N MET A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.543A pdb=" N SER A 157 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 removed outlier: 4.096A pdb=" N MET A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ASN A 193 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP A 194 " --> pdb=" O ARG A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 293 through 327 removed outlier: 3.522A pdb=" N TYR A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.521A pdb=" N LYS A 335 " --> pdb=" O CYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.043A pdb=" N LYS A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 409 removed outlier: 3.667A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 removed outlier: 3.941A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 487 removed outlier: 3.617A pdb=" N CYS A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.694A pdb=" N THR A 509 " --> pdb=" O PRO A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 539 removed outlier: 3.583A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 574 removed outlier: 5.417A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 625 Processing helix chain 'A' and resid 625 through 638 Processing helix chain 'A' and resid 648 through 655 removed outlier: 3.644A pdb=" N HIS A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 Processing helix chain 'A' and resid 687 through 710 removed outlier: 3.549A pdb=" N LEU A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 4.107A pdb=" N ILE A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 4.021A 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 775 through 781 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 825 through 857 Processing helix chain 'A' and resid 861 through 886 removed outlier: 3.740A pdb=" N LEU A 879 " --> pdb=" O THR A 875 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP A 886 " --> pdb=" O SER A 882 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 111 through 116 removed outlier: 3.754A pdb=" N PHE B 73 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 145 through 150 removed outlier: 6.145A pdb=" N ALA B 185 " --> pdb=" O PRO B 147 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS B 149 " --> pdb=" O PHE B 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 223 through 224 removed outlier: 3.908A pdb=" N GLN B 223 " --> pdb=" O LYS B 230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 347 through 348 Processing sheet with id=AA5, first strand: chain 'B' and resid 429 through 432 Processing sheet with id=AA6, first strand: chain 'B' and resid 782 through 785 Processing sheet with id=AA7, first strand: chain 'A' and resid 111 through 116 removed outlier: 3.754A pdb=" N PHE A 73 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 145 through 150 removed outlier: 6.146A pdb=" N ALA A 185 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 149 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.907A pdb=" N GLN A 223 " --> pdb=" O LYS A 230 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 347 through 348 Processing sheet with id=AB2, first strand: chain 'A' and resid 429 through 432 Processing sheet with id=AB3, 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: 2.15 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2166 1.31 - 1.44: 4124 1.44 - 1.57: 8018 1.57 - 1.69: 24 1.69 - 1.82: 124 Bond restraints: 14456 Sorted by residual: bond pdb=" C1 PGW B1005 " pdb=" O01 PGW B1005 " ideal model delta sigma weight residual 1.332 1.425 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C1 PGW A1005 " pdb=" O01 PGW A1005 " ideal model delta sigma weight residual 1.332 1.424 -0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C1 PGW A1004 " pdb=" O01 PGW A1004 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C1 PGW B1004 " pdb=" O01 PGW B1004 " ideal model delta sigma weight residual 1.332 1.421 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C1 PGW A1002 " pdb=" O01 PGW A1002 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.95e+01 ... (remaining 14451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 19062 2.76 - 5.52: 358 5.52 - 8.27: 54 8.27 - 11.03: 50 11.03 - 13.79: 4 Bond angle restraints: 19528 Sorted by residual: angle pdb=" N VAL B 168 " pdb=" CA VAL B 168 " pdb=" C VAL B 168 " ideal model delta sigma weight residual 113.71 108.59 5.12 9.50e-01 1.11e+00 2.90e+01 angle pdb=" N VAL A 168 " pdb=" CA VAL A 168 " pdb=" C VAL A 168 " ideal model delta sigma weight residual 113.71 108.62 5.09 9.50e-01 1.11e+00 2.87e+01 angle pdb=" CB MET B 225 " pdb=" CG MET B 225 " pdb=" SD MET B 225 " ideal model delta sigma weight residual 112.70 126.49 -13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" CB MET A 225 " pdb=" CG MET A 225 " pdb=" SD MET A 225 " ideal model delta sigma weight residual 112.70 126.47 -13.77 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O11 PGW B1001 " pdb=" P PGW B1001 " pdb=" O12 PGW B1001 " ideal model delta sigma weight residual 98.90 110.15 -11.25 3.00e+00 1.11e-01 1.41e+01 ... (remaining 19523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.42: 8202 34.42 - 68.84: 425 68.84 - 103.26: 43 103.26 - 137.68: 14 137.68 - 172.10: 8 Dihedral angle restraints: 8692 sinusoidal: 3770 harmonic: 4922 Sorted by residual: dihedral pdb=" CB CYS A 331 " pdb=" SG CYS A 331 " pdb=" SG CYS A 372 " pdb=" CB CYS A 372 " ideal model delta sinusoidal sigma weight residual -86.00 -160.38 74.38 1 1.00e+01 1.00e-02 7.02e+01 dihedral pdb=" CB CYS B 331 " pdb=" SG CYS B 331 " pdb=" SG CYS B 372 " pdb=" CB CYS B 372 " ideal model delta sinusoidal sigma weight residual -86.00 -160.37 74.37 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" C03 PGW A1002 " pdb=" C01 PGW A1002 " pdb=" C02 PGW A1002 " pdb=" O03 PGW A1002 " ideal model delta sinusoidal sigma weight residual -64.65 107.45 -172.10 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 8689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1472 0.038 - 0.077: 452 0.077 - 0.115: 139 0.115 - 0.153: 14 0.153 - 0.191: 11 Chirality restraints: 2088 Sorted by residual: chirality pdb=" C02 PGW A1001 " pdb=" C01 PGW A1001 " pdb=" C03 PGW A1001 " pdb=" O01 PGW A1001 " both_signs ideal model delta sigma weight residual False 2.36 2.55 -0.19 2.00e-01 2.50e+01 9.15e-01 chirality pdb=" C02 PGW B1001 " pdb=" C01 PGW B1001 " pdb=" C03 PGW B1001 " pdb=" O01 PGW B1001 " both_signs ideal model delta sigma weight residual False 2.36 2.55 -0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" C02 PGW B1003 " pdb=" C01 PGW B1003 " pdb=" C03 PGW B1003 " pdb=" O01 PGW B1003 " both_signs ideal model delta sigma weight residual False 2.36 2.53 -0.18 2.00e-01 2.50e+01 7.84e-01 ... (remaining 2085 not shown) Planarity restraints: 2422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 504 " -0.051 5.00e-02 4.00e+02 7.81e-02 9.76e+00 pdb=" N PRO B 505 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 505 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 505 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 504 " 0.051 5.00e-02 4.00e+02 7.81e-02 9.76e+00 pdb=" N PRO A 505 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 505 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 505 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 762 " -0.039 5.00e-02 4.00e+02 5.82e-02 5.43e+00 pdb=" N PRO A 763 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 763 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 763 " -0.032 5.00e-02 4.00e+02 ... (remaining 2419 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3807 2.81 - 3.33: 13003 3.33 - 3.85: 23827 3.85 - 4.38: 27414 4.38 - 4.90: 47452 Nonbonded interactions: 115503 Sorted by model distance: nonbonded pdb=" O ILE B 762 " pdb=" N GLY B 766 " model vdw 2.283 3.120 nonbonded pdb=" O ILE A 762 " pdb=" N GLY A 766 " model vdw 2.284 3.120 nonbonded pdb=" OG SER B 782 " pdb=" O ASP B 811 " model vdw 2.321 3.040 nonbonded pdb=" OG SER A 782 " pdb=" O ASP A 811 " model vdw 2.322 3.040 nonbonded pdb=" OD2 ASP A 788 " pdb=" OH TYR A 822 " model vdw 2.335 3.040 ... (remaining 115498 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.400 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 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 0.093 14466 Z= 0.243 Angle : 0.907 13.789 19548 Z= 0.368 Chirality : 0.041 0.191 2088 Planarity : 0.005 0.078 2422 Dihedral : 20.656 172.104 5494 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.40 % Allowed : 23.53 % Favored : 76.07 % 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: 1.63 (0.21), residues: 1652 helix: 2.23 (0.17), residues: 902 sheet: 0.11 (0.54), residues: 102 loop : -0.40 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 116 TYR 0.013 0.001 TYR A 306 PHE 0.011 0.001 PHE A 560 TRP 0.014 0.001 TRP A 397 HIS 0.002 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00490 (14456) covalent geometry : angle 0.90600 (19528) SS BOND : bond 0.00100 ( 10) SS BOND : angle 1.31092 ( 20) hydrogen bonds : bond 0.11621 ( 734) hydrogen bonds : angle 5.47970 ( 2142) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 729 MET cc_start: 0.7744 (mmm) cc_final: 0.7518 (tpt) REVERT: A 729 MET cc_start: 0.7682 (mmm) cc_final: 0.7442 (tpt) outliers start: 6 outliers final: 6 residues processed: 146 average time/residue: 0.6766 time to fit residues: 107.3221 Evaluate side-chains 141 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 135 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 823 LYS Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 823 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 ASN B 104 ASN B 143 HIS B 223 GLN B 234 ASN B 308 GLN B 328 GLN B 414 GLN B 415 GLN B 429 HIS B 657 GLN B 796 ASN B 818 HIS ** B 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 ASN A 104 ASN A 143 HIS A 223 GLN A 234 ASN A 308 GLN A 328 GLN A 414 GLN A 415 GLN A 426 GLN A 429 HIS A 657 GLN A 796 ASN A 818 HIS ** A 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.148639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.094312 restraints weight = 14579.128| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.45 r_work: 0.2906 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14466 Z= 0.199 Angle : 0.601 8.514 19548 Z= 0.308 Chirality : 0.044 0.174 2088 Planarity : 0.005 0.065 2422 Dihedral : 18.632 178.472 2190 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.75 % Allowed : 19.45 % Favored : 75.80 % 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: 1.16 (0.20), residues: 1652 helix: 1.90 (0.16), residues: 906 sheet: -0.26 (0.52), residues: 102 loop : -0.68 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 116 TYR 0.014 0.001 TYR A 306 PHE 0.013 0.002 PHE B 556 TRP 0.012 0.002 TRP A 829 HIS 0.005 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00492 (14456) covalent geometry : angle 0.59823 (19528) SS BOND : bond 0.00334 ( 10) SS BOND : angle 1.83454 ( 20) hydrogen bonds : bond 0.05215 ( 734) hydrogen bonds : angle 4.50774 ( 2142) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 148 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 298 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7459 (tt) REVERT: B 530 LYS cc_start: 0.6384 (OUTLIER) cc_final: 0.5785 (mptt) REVERT: B 670 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.5997 (mp0) REVERT: B 729 MET cc_start: 0.7715 (mmm) cc_final: 0.7442 (tpt) REVERT: B 842 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6442 (ttt) REVERT: A 298 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7416 (tt) REVERT: A 530 LYS cc_start: 0.6315 (OUTLIER) cc_final: 0.5729 (mptt) REVERT: A 729 MET cc_start: 0.7727 (mmm) cc_final: 0.7458 (tpt) REVERT: A 842 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6432 (ttt) outliers start: 71 outliers final: 18 residues processed: 195 average time/residue: 0.6303 time to fit residues: 134.1295 Evaluate side-chains 164 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 670 GLU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 842 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 2 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 HIS ** B 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 ASN A 429 HIS ** A 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.144747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.090941 restraints weight = 14814.721| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.43 r_work: 0.2857 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 14466 Z= 0.283 Angle : 0.664 9.163 19548 Z= 0.342 Chirality : 0.047 0.183 2088 Planarity : 0.005 0.071 2422 Dihedral : 17.655 174.127 2186 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.81 % Allowed : 19.45 % Favored : 75.74 % 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: 0.67 (0.20), residues: 1652 helix: 1.43 (0.16), residues: 928 sheet: -0.55 (0.51), residues: 102 loop : -0.86 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 116 TYR 0.015 0.002 TYR A 306 PHE 0.014 0.002 PHE A 556 TRP 0.015 0.002 TRP A 273 HIS 0.004 0.001 HIS B 818 Details of bonding type rmsd covalent geometry : bond 0.00715 (14456) covalent geometry : angle 0.66066 (19528) SS BOND : bond 0.00503 ( 10) SS BOND : angle 2.18443 ( 20) hydrogen bonds : bond 0.05871 ( 734) hydrogen bonds : angle 4.63671 ( 2142) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 144 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7121 (t80) REVERT: B 75 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6821 (mt) REVERT: B 173 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6276 (mm-30) REVERT: B 258 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7818 (mm-30) REVERT: B 530 LYS cc_start: 0.6451 (OUTLIER) cc_final: 0.5729 (mptt) REVERT: B 633 LEU cc_start: 0.6079 (OUTLIER) cc_final: 0.5697 (mm) REVERT: B 670 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.6206 (mp0) REVERT: B 730 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6969 (mt0) REVERT: B 750 MET cc_start: 0.7655 (ttp) cc_final: 0.7416 (ttp) REVERT: B 842 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6636 (ttt) REVERT: A 73 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7122 (t80) REVERT: A 75 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6812 (mt) REVERT: A 173 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.6283 (mm-30) REVERT: A 530 LYS cc_start: 0.6472 (OUTLIER) cc_final: 0.5733 (mptt) REVERT: A 670 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6190 (mp0) REVERT: A 730 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6982 (mt0) REVERT: A 750 MET cc_start: 0.7669 (ttp) cc_final: 0.7432 (ttp) REVERT: A 842 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.6617 (ttt) REVERT: A 850 LYS cc_start: 0.6565 (OUTLIER) cc_final: 0.6341 (ttpt) outliers start: 72 outliers final: 25 residues processed: 200 average time/residue: 0.6992 time to fit residues: 151.4767 Evaluate side-chains 183 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 670 GLU Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 823 LYS Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 850 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 116 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 161 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 HIS ** B 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 GLN A 234 ASN A 429 HIS ** A 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.149567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.096559 restraints weight = 14647.641| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.43 r_work: 0.2943 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14466 Z= 0.112 Angle : 0.527 8.257 19548 Z= 0.274 Chirality : 0.041 0.186 2088 Planarity : 0.005 0.065 2422 Dihedral : 16.726 175.427 2186 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.48 % Allowed : 20.59 % Favored : 75.94 % 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: 1.15 (0.20), residues: 1652 helix: 1.89 (0.16), residues: 906 sheet: -0.15 (0.57), residues: 82 loop : -0.70 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 116 TYR 0.013 0.001 TYR B 580 PHE 0.012 0.001 PHE A 556 TRP 0.012 0.001 TRP B 829 HIS 0.003 0.001 HIS B 880 Details of bonding type rmsd covalent geometry : bond 0.00249 (14456) covalent geometry : angle 0.52475 (19528) SS BOND : bond 0.00184 ( 10) SS BOND : angle 1.51053 ( 20) hydrogen bonds : bond 0.04349 ( 734) hydrogen bonds : angle 4.33955 ( 2142) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 151 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7520 (m-80) REVERT: B 75 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6373 (mt) REVERT: B 173 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.6128 (mm-30) REVERT: B 258 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7692 (mm-30) REVERT: B 400 ARG cc_start: 0.6365 (OUTLIER) cc_final: 0.6130 (mmm160) REVERT: B 530 LYS cc_start: 0.6261 (OUTLIER) cc_final: 0.5744 (mptt) REVERT: B 633 LEU cc_start: 0.6036 (OUTLIER) cc_final: 0.5659 (mm) REVERT: B 730 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6775 (mt0) REVERT: B 750 MET cc_start: 0.7484 (ttp) cc_final: 0.7226 (ttp) REVERT: B 842 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6165 (ttt) REVERT: A 73 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7524 (m-80) REVERT: A 75 LEU cc_start: 0.6791 (OUTLIER) cc_final: 0.6365 (mt) REVERT: A 258 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7960 (mm-30) REVERT: A 400 ARG cc_start: 0.6382 (OUTLIER) cc_final: 0.6144 (mmm160) REVERT: A 530 LYS cc_start: 0.6325 (OUTLIER) cc_final: 0.5806 (mptt) REVERT: A 730 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6800 (mt0) REVERT: A 750 MET cc_start: 0.7470 (ttp) cc_final: 0.7227 (ttp) REVERT: A 842 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6138 (ttt) outliers start: 52 outliers final: 15 residues processed: 193 average time/residue: 0.6199 time to fit residues: 131.0116 Evaluate side-chains 178 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 848 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 101 optimal weight: 7.9990 chunk 137 optimal weight: 0.5980 chunk 133 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 ASN B 429 HIS ** B 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 HIS ** A 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.147286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.093862 restraints weight = 14671.645| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.43 r_work: 0.2904 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14466 Z= 0.175 Angle : 0.575 8.474 19548 Z= 0.297 Chirality : 0.043 0.201 2088 Planarity : 0.005 0.071 2422 Dihedral : 16.603 177.144 2182 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.08 % Allowed : 20.72 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.04 (0.20), residues: 1652 helix: 1.79 (0.16), residues: 918 sheet: -0.24 (0.56), residues: 82 loop : -0.77 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 116 TYR 0.011 0.001 TYR B 306 PHE 0.014 0.001 PHE B 556 TRP 0.013 0.001 TRP A 829 HIS 0.012 0.001 HIS A 880 Details of bonding type rmsd covalent geometry : bond 0.00430 (14456) covalent geometry : angle 0.57198 (19528) SS BOND : bond 0.00241 ( 10) SS BOND : angle 1.91373 ( 20) hydrogen bonds : bond 0.04925 ( 734) hydrogen bonds : angle 4.42128 ( 2142) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 148 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.7539 (m-80) REVERT: B 75 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6500 (mt) REVERT: B 173 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6215 (mm-30) REVERT: B 258 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7732 (mm-30) REVERT: B 530 LYS cc_start: 0.6267 (OUTLIER) cc_final: 0.5697 (mptt) REVERT: B 633 LEU cc_start: 0.6017 (OUTLIER) cc_final: 0.5631 (mm) REVERT: B 730 GLN cc_start: 0.7021 (OUTLIER) cc_final: 0.6799 (mt0) REVERT: B 750 MET cc_start: 0.7568 (ttp) cc_final: 0.6635 (tpt) REVERT: B 842 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6377 (ttt) REVERT: A 73 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.7549 (m-80) REVERT: A 75 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6527 (mt) REVERT: A 258 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.8023 (mm-30) REVERT: A 530 LYS cc_start: 0.6280 (OUTLIER) cc_final: 0.5705 (mptt) REVERT: A 670 GLU cc_start: 0.6379 (OUTLIER) cc_final: 0.5984 (mp0) REVERT: A 730 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.6814 (mt0) REVERT: A 750 MET cc_start: 0.7544 (ttp) cc_final: 0.6593 (tpt) REVERT: A 842 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6372 (ttt) outliers start: 61 outliers final: 23 residues processed: 197 average time/residue: 0.6763 time to fit residues: 144.6738 Evaluate side-chains 182 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 848 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 112 optimal weight: 0.0670 chunk 22 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 115 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 0.9980 chunk 142 optimal weight: 0.4980 chunk 32 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS ** B 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 HIS ** A 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.152767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.098545 restraints weight = 14636.415| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.48 r_work: 0.2977 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14466 Z= 0.101 Angle : 0.510 9.275 19548 Z= 0.263 Chirality : 0.041 0.216 2088 Planarity : 0.005 0.067 2422 Dihedral : 15.890 179.056 2182 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.94 % Allowed : 22.33 % Favored : 74.73 % 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: 1.30 (0.20), residues: 1652 helix: 2.05 (0.16), residues: 900 sheet: -0.29 (0.56), residues: 82 loop : -0.63 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.014 0.001 TYR B 580 PHE 0.011 0.001 PHE B 556 TRP 0.011 0.001 TRP A 397 HIS 0.011 0.001 HIS A 880 Details of bonding type rmsd covalent geometry : bond 0.00214 (14456) covalent geometry : angle 0.50827 (19528) SS BOND : bond 0.00125 ( 10) SS BOND : angle 1.43091 ( 20) hydrogen bonds : bond 0.03998 ( 734) hydrogen bonds : angle 4.25748 ( 2142) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7619 (m-80) REVERT: B 75 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6409 (mt) REVERT: B 113 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: B 258 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7738 (mm-30) REVERT: B 530 LYS cc_start: 0.6291 (OUTLIER) cc_final: 0.5854 (mptt) REVERT: B 730 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6834 (mt0) REVERT: B 750 MET cc_start: 0.7531 (ttp) cc_final: 0.6571 (tpt) REVERT: B 842 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6175 (ttt) REVERT: A 73 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: A 75 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6437 (mt) REVERT: A 113 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: A 173 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.6134 (mm-30) REVERT: A 258 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8040 (mm-30) REVERT: A 530 LYS cc_start: 0.6296 (OUTLIER) cc_final: 0.5859 (mptt) REVERT: A 730 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6827 (mt0) REVERT: A 750 MET cc_start: 0.7496 (ttp) cc_final: 0.6573 (tpt) REVERT: A 842 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6144 (ttt) outliers start: 44 outliers final: 12 residues processed: 183 average time/residue: 0.6124 time to fit residues: 122.7130 Evaluate side-chains 172 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 842 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 130 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 18 optimal weight: 0.0470 chunk 123 optimal weight: 0.0070 chunk 46 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 overall best weight: 2.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 ASN B 308 GLN B 429 HIS ** B 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 GLN A 429 HIS ** A 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.148667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.093795 restraints weight = 14688.642| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.49 r_work: 0.2903 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14466 Z= 0.183 Angle : 0.583 9.622 19548 Z= 0.299 Chirality : 0.043 0.250 2088 Planarity : 0.005 0.076 2422 Dihedral : 15.976 179.563 2178 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.48 % Allowed : 21.66 % Favored : 74.87 % 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: 1.12 (0.20), residues: 1652 helix: 1.87 (0.16), residues: 918 sheet: -0.41 (0.55), residues: 82 loop : -0.74 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 116 TYR 0.013 0.001 TYR A 306 PHE 0.013 0.001 PHE B 556 TRP 0.012 0.002 TRP A 829 HIS 0.011 0.001 HIS A 880 Details of bonding type rmsd covalent geometry : bond 0.00449 (14456) covalent geometry : angle 0.57971 (19528) SS BOND : bond 0.00243 ( 10) SS BOND : angle 2.03958 ( 20) hydrogen bonds : bond 0.04936 ( 734) hydrogen bonds : angle 4.39134 ( 2142) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: B 75 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6528 (mt) REVERT: B 258 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7742 (mm-30) REVERT: B 347 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7346 (tm) REVERT: B 464 ILE cc_start: 0.6483 (OUTLIER) cc_final: 0.6116 (mp) REVERT: B 530 LYS cc_start: 0.6296 (OUTLIER) cc_final: 0.5725 (mptt) REVERT: B 633 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5595 (mm) REVERT: B 750 MET cc_start: 0.7571 (ttp) cc_final: 0.6632 (tpt) REVERT: B 842 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6451 (ttt) REVERT: A 73 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: A 75 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6561 (mt) REVERT: A 258 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8032 (mm-30) REVERT: A 347 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7347 (tm) REVERT: A 530 LYS cc_start: 0.6306 (OUTLIER) cc_final: 0.5734 (mptt) REVERT: A 750 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.6645 (tpt) REVERT: A 842 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6449 (ttt) outliers start: 52 outliers final: 20 residues processed: 188 average time/residue: 0.6222 time to fit residues: 128.0615 Evaluate side-chains 180 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 848 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 33 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 57 optimal weight: 0.4980 chunk 146 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 HIS ** B 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 HIS ** A 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.148739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.095688 restraints weight = 14637.278| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.42 r_work: 0.2932 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14466 Z= 0.141 Angle : 0.554 9.992 19548 Z= 0.284 Chirality : 0.042 0.331 2088 Planarity : 0.005 0.076 2422 Dihedral : 15.575 179.292 2178 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.21 % Allowed : 21.99 % Favored : 74.80 % 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: 1.19 (0.20), residues: 1652 helix: 1.96 (0.16), residues: 900 sheet: -0.40 (0.55), residues: 82 loop : -0.68 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 116 TYR 0.011 0.001 TYR A 306 PHE 0.013 0.001 PHE B 556 TRP 0.011 0.001 TRP B 829 HIS 0.010 0.001 HIS A 880 Details of bonding type rmsd covalent geometry : bond 0.00337 (14456) covalent geometry : angle 0.55135 (19528) SS BOND : bond 0.00192 ( 10) SS BOND : angle 1.76254 ( 20) hydrogen bonds : bond 0.04566 ( 734) hydrogen bonds : angle 4.33833 ( 2142) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 140 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7636 (m-80) REVERT: B 75 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6528 (mt) REVERT: B 258 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7788 (mm-30) REVERT: B 347 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7319 (tm) REVERT: B 530 LYS cc_start: 0.6392 (OUTLIER) cc_final: 0.5868 (mptt) REVERT: B 633 LEU cc_start: 0.6011 (OUTLIER) cc_final: 0.5635 (mm) REVERT: B 730 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6919 (mt0) REVERT: B 750 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.6614 (tpt) REVERT: B 842 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6364 (ttt) REVERT: A 73 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.7651 (m-80) REVERT: A 75 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6549 (mt) REVERT: A 173 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6270 (mm-30) REVERT: A 258 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8049 (mm-30) REVERT: A 347 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7324 (tm) REVERT: A 530 LYS cc_start: 0.6388 (OUTLIER) cc_final: 0.5861 (mptt) REVERT: A 670 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.6012 (mp0) REVERT: A 730 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6929 (mt0) REVERT: A 750 MET cc_start: 0.7557 (ttp) cc_final: 0.6628 (tpt) REVERT: A 842 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6364 (ttt) outliers start: 48 outliers final: 22 residues processed: 178 average time/residue: 0.6272 time to fit residues: 122.3459 Evaluate side-chains 179 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 848 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 49 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 HIS ** B 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 HIS ** A 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.145533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.092337 restraints weight = 14791.488| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.41 r_work: 0.2881 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 14466 Z= 0.238 Angle : 0.633 10.626 19548 Z= 0.325 Chirality : 0.046 0.223 2088 Planarity : 0.005 0.083 2422 Dihedral : 15.939 179.117 2178 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.69 % Favored : 96.19 % Rotamer: Outliers : 3.14 % Allowed : 22.33 % Favored : 74.53 % 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: 0.90 (0.20), residues: 1652 helix: 1.64 (0.16), residues: 920 sheet: -0.49 (0.55), residues: 82 loop : -0.76 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 116 TYR 0.015 0.002 TYR B 306 PHE 0.013 0.002 PHE B 556 TRP 0.013 0.002 TRP A 273 HIS 0.010 0.001 HIS A 880 Details of bonding type rmsd covalent geometry : bond 0.00597 (14456) covalent geometry : angle 0.62912 (19528) SS BOND : bond 0.00317 ( 10) SS BOND : angle 2.31268 ( 20) hydrogen bonds : bond 0.05437 ( 734) hydrogen bonds : angle 4.50597 ( 2142) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 142 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: B 75 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6669 (mt) REVERT: B 258 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7867 (mm-30) REVERT: B 347 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7406 (tm) REVERT: B 530 LYS cc_start: 0.6426 (OUTLIER) cc_final: 0.5694 (mptt) REVERT: B 633 LEU cc_start: 0.6012 (OUTLIER) cc_final: 0.5647 (mm) REVERT: B 670 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6109 (mp0) REVERT: B 750 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.6776 (tpt) REVERT: B 842 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.6618 (ttt) REVERT: A 73 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7560 (m-80) REVERT: A 75 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6691 (mt) REVERT: A 258 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8109 (mm-30) REVERT: A 347 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7410 (tm) REVERT: A 530 LYS cc_start: 0.6434 (OUTLIER) cc_final: 0.5790 (mptt) REVERT: A 670 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6110 (mp0) REVERT: A 750 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.6768 (tpt) REVERT: A 842 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.6611 (ttt) outliers start: 47 outliers final: 24 residues processed: 175 average time/residue: 0.7076 time to fit residues: 134.4730 Evaluate side-chains 181 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 670 GLU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 848 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 85 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 154 optimal weight: 0.9980 chunk 153 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 93 optimal weight: 0.0030 chunk 133 optimal weight: 2.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 HIS ** A 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.151096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.096568 restraints weight = 14682.126| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.51 r_work: 0.2946 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14466 Z= 0.115 Angle : 0.540 11.769 19548 Z= 0.277 Chirality : 0.041 0.277 2088 Planarity : 0.005 0.078 2422 Dihedral : 15.111 175.788 2178 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.57 % Favored : 96.31 % Rotamer: Outliers : 3.07 % Allowed : 22.53 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.20), residues: 1652 helix: 1.95 (0.16), residues: 900 sheet: -0.49 (0.54), residues: 82 loop : -0.69 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 116 TYR 0.013 0.001 TYR B 580 PHE 0.013 0.001 PHE A 556 TRP 0.012 0.001 TRP B 397 HIS 0.011 0.001 HIS A 880 Details of bonding type rmsd covalent geometry : bond 0.00261 (14456) covalent geometry : angle 0.53828 (19528) SS BOND : bond 0.00125 ( 10) SS BOND : angle 1.45908 ( 20) hydrogen bonds : bond 0.04265 ( 734) hydrogen bonds : angle 4.29678 ( 2142) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: B 75 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6336 (mt) REVERT: B 113 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: B 258 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7713 (mm-30) REVERT: B 347 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7142 (tm) REVERT: B 530 LYS cc_start: 0.6272 (OUTLIER) cc_final: 0.5815 (mptt) REVERT: B 633 LEU cc_start: 0.6006 (OUTLIER) cc_final: 0.5635 (mm) REVERT: B 730 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6822 (mt0) REVERT: B 750 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.6521 (tpt) REVERT: B 842 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6153 (ttt) REVERT: A 73 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: A 75 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6362 (mt) REVERT: A 113 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: A 258 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7959 (mm-30) REVERT: A 347 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7162 (tm) REVERT: A 530 LYS cc_start: 0.6283 (OUTLIER) cc_final: 0.5830 (mptt) REVERT: A 730 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6838 (mt0) REVERT: A 750 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.6506 (tpt) REVERT: A 842 MET cc_start: 0.7004 (OUTLIER) cc_final: 0.6121 (ttt) outliers start: 46 outliers final: 20 residues processed: 176 average time/residue: 0.6639 time to fit residues: 127.4816 Evaluate side-chains 182 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 848 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 9 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 139 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 426 GLN B 429 HIS ** B 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 HIS ** A 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.095501 restraints weight = 14556.582| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.41 r_work: 0.2928 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14466 Z= 0.147 Angle : 0.565 11.484 19548 Z= 0.290 Chirality : 0.043 0.336 2088 Planarity : 0.005 0.080 2422 Dihedral : 14.871 175.753 2178 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.87 % Favored : 96.00 % Rotamer: Outliers : 3.07 % Allowed : 22.33 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.15 (0.20), residues: 1652 helix: 1.94 (0.16), residues: 900 sheet: -0.57 (0.54), residues: 82 loop : -0.70 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 441 TYR 0.012 0.001 TYR A 306 PHE 0.013 0.001 PHE A 556 TRP 0.012 0.001 TRP B 829 HIS 0.005 0.001 HIS B 880 Details of bonding type rmsd covalent geometry : bond 0.00355 (14456) covalent geometry : angle 0.56258 (19528) SS BOND : bond 0.00196 ( 10) SS BOND : angle 1.76573 ( 20) hydrogen bonds : bond 0.04608 ( 734) hydrogen bonds : angle 4.33162 ( 2142) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5902.80 seconds wall clock time: 101 minutes 3.55 seconds (6063.55 seconds total)