Starting phenix.real_space_refine on Mon May 4 09:16:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yrg_73367/05_2026/9yrg_73367.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yrg_73367/05_2026/9yrg_73367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yrg_73367/05_2026/9yrg_73367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yrg_73367/05_2026/9yrg_73367.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yrg_73367/05_2026/9yrg_73367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yrg_73367/05_2026/9yrg_73367.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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 6 5.49 5 S 112 5.16 5 C 12338 2.51 5 N 3300 2.21 5 O 3687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s 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: 19443 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 912, 7387 Classifications: {'peptide': 912} Link IDs: {'PTRANS': 31, 'TRANS': 880} Chain breaks: 2 Chain: "B" Number of atoms: 7362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 7362 Classifications: {'peptide': 908} Link IDs: {'PTRANS': 31, 'TRANS': 876} Chain breaks: 2 Chain: "C" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1188 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Chain: "D" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1188 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Chain: "E" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1127 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "F" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1127 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.14, per 1000 atoms: 0.26 Number of scatterers: 19443 At special positions: 0 Unit cell: (91.3, 173.47, 179.28, 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 112 16.00 P 6 15.00 O 3687 8.00 N 3300 7.00 C 12338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 905 " - pdb=" SG CYS B 905 " 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: 2.04 Conformation dependent library (CDL) restraints added in 914.6 milliseconds 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4532 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 13 sheets defined 62.4% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 removed outlier: 3.834A pdb=" N ALA A 7 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ALA A 11 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 12 " --> pdb=" O PHE A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 26 Processing helix chain 'A' and resid 27 through 29 No H-bonds generated for 'chain 'A' and resid 27 through 29' Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 97 through 111 removed outlier: 3.757A pdb=" N SER A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 142 Processing helix chain 'A' and resid 146 through 150 removed outlier: 3.506A pdb=" N ALA A 150 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 183 through 201 Processing helix chain 'A' and resid 216 through 231 removed outlier: 4.351A pdb=" N ASN A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Proline residue: A 225 - end of helix removed outlier: 3.780A pdb=" N PHE A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 283 through 290 removed outlier: 4.260A pdb=" N TYR A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 removed outlier: 4.026A pdb=" N LEU A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.628A pdb=" N GLU A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 360 removed outlier: 3.815A pdb=" N GLY A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.740A pdb=" N ASN A 408 " --> pdb=" O LYS A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 448 Processing helix chain 'A' and resid 472 through 494 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 529 through 540 Processing helix chain 'A' and resid 544 through 557 Processing helix chain 'A' and resid 592 through 599 Processing helix chain 'A' and resid 602 through 611 Processing helix chain 'A' and resid 614 through 622 Processing helix chain 'A' and resid 646 through 662 Processing helix chain 'A' and resid 663 through 665 No H-bonds generated for 'chain 'A' and resid 663 through 665' Processing helix chain 'A' and resid 685 through 697 Processing helix chain 'A' and resid 697 through 707 Processing helix chain 'A' and resid 714 through 722 Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'A' and resid 737 through 749 Processing helix chain 'A' and resid 768 through 781 Processing helix chain 'A' and resid 781 through 825 Processing helix chain 'A' and resid 827 through 837 Processing helix chain 'A' and resid 838 through 840 No H-bonds generated for 'chain 'A' and resid 838 through 840' Processing helix chain 'A' and resid 844 through 943 Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 19 through 29 removed outlier: 3.552A pdb=" N ARG B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 58 removed outlier: 4.154A pdb=" N GLY B 57 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS B 58 " --> pdb=" O GLU B 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 54 through 58' Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.909A pdb=" N LEU B 93 " --> pdb=" O MET B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 111 Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 183 through 196 Processing helix chain 'B' and resid 216 through 232 removed outlier: 3.887A pdb=" N ASN B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Proline residue: B 225 - end of helix Processing helix chain 'B' and resid 270 through 275 removed outlier: 4.407A pdb=" N ILE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 270 through 275' Processing helix chain 'B' and resid 283 through 291 removed outlier: 3.933A pdb=" N TYR B 287 " --> pdb=" O TYR B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 302 removed outlier: 3.593A pdb=" N ASP B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 340 Processing helix chain 'B' and resid 342 through 362 Processing helix chain 'B' and resid 378 through 389 Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.576A pdb=" N HIS B 401 " --> pdb=" O LYS B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 447 Processing helix chain 'B' and resid 472 through 492 Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 517 through 526 removed outlier: 3.532A pdb=" N ILE B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE B 524 " --> pdb=" O CYS B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 540 Processing helix chain 'B' and resid 544 through 557 Processing helix chain 'B' and resid 592 through 598 removed outlier: 4.024A pdb=" N ASN B 597 " --> pdb=" O LEU B 594 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 598 " --> pdb=" O GLN B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 612 Processing helix chain 'B' and resid 614 through 620 Processing helix chain 'B' and resid 646 through 663 Processing helix chain 'B' and resid 685 through 697 removed outlier: 3.583A pdb=" N GLY B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 708 Processing helix chain 'B' and resid 715 through 723 Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 738 through 749 Processing helix chain 'B' and resid 768 through 826 removed outlier: 3.807A pdb=" N ASN B 826 " --> pdb=" O MET B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 833 Processing helix chain 'B' and resid 837 through 841 Processing helix chain 'B' and resid 842 through 943 Processing helix chain 'C' and resid 42 through 57 Processing helix chain 'C' and resid 66 through 76 removed outlier: 4.225A pdb=" N GLY C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 94 through 98 removed outlier: 4.370A pdb=" N ASN C 98 " --> pdb=" O GLU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 117 Proline residue: C 109 - end of helix Processing helix chain 'C' and resid 123 through 132 removed outlier: 3.701A pdb=" N VAL C 132 " --> pdb=" O GLU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 153 Processing helix chain 'C' and resid 158 through 166 Processing helix chain 'C' and resid 177 through 185 Processing helix chain 'D' and resid 42 through 57 removed outlier: 3.549A pdb=" N GLN D 46 " --> pdb=" O SER D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 76 removed outlier: 4.513A pdb=" N ASP D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 93 through 100 removed outlier: 4.294A pdb=" N ASN D 98 " --> pdb=" O ASN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 107 through 118 removed outlier: 4.258A pdb=" N MET D 111 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS D 118 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 134 removed outlier: 3.530A pdb=" N PHE D 126 " --> pdb=" O GLY D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 153 removed outlier: 3.815A pdb=" N THR D 152 " --> pdb=" O HIS D 148 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 153 " --> pdb=" O VAL D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 167 Processing helix chain 'D' and resid 177 through 186 Processing helix chain 'E' and resid 23 through 38 Processing helix chain 'E' and resid 46 through 57 removed outlier: 3.815A pdb=" N MET E 57 " --> pdb=" O THR E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 74 removed outlier: 3.563A pdb=" N LYS E 72 " --> pdb=" O ASP E 68 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 89 Processing helix chain 'E' and resid 96 through 108 removed outlier: 3.592A pdb=" N ILE E 100 " --> pdb=" O PRO E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 124 removed outlier: 3.515A pdb=" N LEU E 120 " --> pdb=" O LYS E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 132 through 140 removed outlier: 3.740A pdb=" N ILE E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 162 removed outlier: 4.057A pdb=" N ILE E 156 " --> pdb=" O ASP E 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 31 Processing helix chain 'F' and resid 32 through 37 removed outlier: 3.676A pdb=" N VAL F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 32 through 37' Processing helix chain 'F' and resid 47 through 50 Processing helix chain 'F' and resid 51 through 56 Processing helix chain 'F' and resid 63 through 74 removed outlier: 3.626A pdb=" N LEU F 67 " --> pdb=" O LYS F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 92 removed outlier: 4.371A pdb=" N LEU F 84 " --> pdb=" O PHE F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 108 Processing helix chain 'F' and resid 116 through 128 removed outlier: 4.115A pdb=" N CYS F 128 " --> pdb=" O LEU F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 143 Processing helix chain 'F' and resid 152 through 159 removed outlier: 4.014A pdb=" N ILE F 156 " --> pdb=" O ASP F 152 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 7.010A pdb=" N THR A 60 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 117 removed outlier: 6.501A pdb=" N CYS A 122 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE A 673 " --> pdb=" O CYS A 122 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR A 124 " --> pdb=" O ILE A 673 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 455 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 248 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER A 260 " --> pdb=" O HIS A 251 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA4, first strand: chain 'A' and resid 364 through 366 Processing sheet with id=AA5, first strand: chain 'A' and resid 563 through 564 Processing sheet with id=AA6, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.597A pdb=" N ASN A 711 " --> pdb=" O PHE A 765 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 68 through 70 removed outlier: 7.213A pdb=" N THR B 60 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET B 77 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 116 through 117 removed outlier: 6.576A pdb=" N CYS B 122 " --> pdb=" O ARG B 671 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ILE B 673 " --> pdb=" O CYS B 122 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N THR B 124 " --> pdb=" O ILE B 673 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER B 173 " --> pdb=" O HIS B 668 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL B 670 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU B 175 " --> pdb=" O VAL B 670 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N CYS B 672 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR B 177 " --> pdb=" O CYS B 672 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLN B 172 " --> pdb=" O GLY B 458 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N LEU B 460 " --> pdb=" O GLN B 172 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE B 174 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP B 262 " --> pdb=" O ARG B 249 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 563 through 564 Processing sheet with id=AB1, first strand: chain 'B' and resid 712 through 714 Processing sheet with id=AB2, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AB3, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AB4, first strand: chain 'D' and resid 141 through 142 removed outlier: 3.564A pdb=" N VAL D 141 " --> pdb=" O ILE D 176 " (cutoff:3.500A) 1089 hydrogen bonds defined for protein. 3135 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: 3.49 Time building geometry restraints manager: 2.55 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: 3367 1.31 - 1.44: 4937 1.44 - 1.56: 11291 1.56 - 1.69: 7 1.69 - 1.82: 198 Bond restraints: 19800 Sorted by residual: bond pdb=" C LEU A 496 " pdb=" N GLU A 497 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.20e-02 6.94e+03 1.02e+02 bond pdb=" C GLU A 497 " pdb=" N GLN A 498 " ideal model delta sigma weight residual 1.335 1.227 0.108 1.38e-02 5.25e+03 6.11e+01 bond pdb=" CG ASP E 49 " pdb=" OD2 ASP E 49 " ideal model delta sigma weight residual 1.249 1.330 -0.081 1.90e-02 2.77e+03 1.82e+01 bond pdb=" CG ASP B 282 " pdb=" OD2 ASP B 282 " ideal model delta sigma weight residual 1.249 1.330 -0.081 1.90e-02 2.77e+03 1.80e+01 bond pdb=" CG ASP A 282 " pdb=" OD2 ASP A 282 " ideal model delta sigma weight residual 1.249 1.326 -0.077 1.90e-02 2.77e+03 1.66e+01 ... (remaining 19795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 25617 2.08 - 4.16: 930 4.16 - 6.24: 75 6.24 - 8.32: 10 8.32 - 10.40: 4 Bond angle restraints: 26636 Sorted by residual: angle pdb=" O LEU A 496 " pdb=" C LEU A 496 " pdb=" N GLU A 497 " ideal model delta sigma weight residual 122.12 130.49 -8.37 1.06e+00 8.90e-01 6.23e+01 angle pdb=" N ILE A 521 " pdb=" CA ILE A 521 " pdb=" C ILE A 521 " ideal model delta sigma weight residual 112.80 106.23 6.57 1.15e+00 7.56e-01 3.26e+01 angle pdb=" N CYS A 520 " pdb=" CA CYS A 520 " pdb=" C CYS A 520 " ideal model delta sigma weight residual 114.31 107.38 6.93 1.29e+00 6.01e-01 2.88e+01 angle pdb=" CA LEU A 496 " pdb=" C LEU A 496 " pdb=" N GLU A 497 " ideal model delta sigma weight residual 117.30 111.23 6.07 1.16e+00 7.43e-01 2.74e+01 angle pdb=" N ASP A 522 " pdb=" CA ASP A 522 " pdb=" C ASP A 522 " ideal model delta sigma weight residual 113.97 107.60 6.37 1.28e+00 6.10e-01 2.47e+01 ... (remaining 26631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 10538 17.84 - 35.67: 1174 35.67 - 53.51: 266 53.51 - 71.34: 93 71.34 - 89.18: 29 Dihedral angle restraints: 12100 sinusoidal: 5096 harmonic: 7004 Sorted by residual: dihedral pdb=" CB CYS A 905 " pdb=" SG CYS A 905 " pdb=" SG CYS B 905 " pdb=" CB CYS B 905 " ideal model delta sinusoidal sigma weight residual -86.00 -142.92 56.92 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CA CYS A 905 " pdb=" CB CYS A 905 " pdb=" SG CYS A 905 " pdb=" SG CYS B 905 " ideal model delta sinusoidal sigma weight residual 79.00 14.31 64.69 1 2.00e+01 2.50e-03 1.37e+01 dihedral pdb=" C5' ADP B1401 " pdb=" O5' ADP B1401 " pdb=" PA ADP B1401 " pdb=" O2A ADP B1401 " ideal model delta sinusoidal sigma weight residual -60.00 1.57 -61.56 1 2.00e+01 2.50e-03 1.26e+01 ... (remaining 12097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2277 0.050 - 0.101: 416 0.101 - 0.151: 157 0.151 - 0.202: 27 0.202 - 0.252: 9 Chirality restraints: 2886 Sorted by residual: chirality pdb=" CA LYS A 707 " pdb=" N LYS A 707 " pdb=" C LYS A 707 " pdb=" CB LYS A 707 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ARG B 712 " pdb=" N ARG B 712 " pdb=" C ARG B 712 " pdb=" CB ARG B 712 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ILE A 157 " pdb=" N ILE A 157 " pdb=" C ILE A 157 " pdb=" CB ILE A 157 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2883 not shown) Planarity restraints: 3459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 712 " -0.523 9.50e-02 1.11e+02 2.34e-01 3.35e+01 pdb=" NE ARG A 712 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 712 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 712 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 712 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 403 " -0.351 9.50e-02 1.11e+02 1.57e-01 1.52e+01 pdb=" NE ARG A 403 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 403 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 403 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 403 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 663 " -0.325 9.50e-02 1.11e+02 1.46e-01 1.31e+01 pdb=" NE ARG B 663 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG B 663 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 663 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 663 " -0.010 2.00e-02 2.50e+03 ... (remaining 3456 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 168 2.53 - 3.12: 16178 3.12 - 3.72: 31675 3.72 - 4.31: 43672 4.31 - 4.90: 71846 Nonbonded interactions: 163539 Sorted by model distance: nonbonded pdb=" O LEU C 73 " pdb=" OG1 THR C 78 " model vdw 1.941 3.040 nonbonded pdb=" N GLU F 65 " pdb=" OE1 GLU F 65 " model vdw 2.125 3.120 nonbonded pdb=" O GLU A 179 " pdb=" NZ LYS A 184 " model vdw 2.126 3.120 nonbonded pdb=" NZ LYS B 837 " pdb=" O ALA F 33 " model vdw 2.145 3.120 nonbonded pdb=" NH2 ARG B 272 " pdb=" OE1 GLU B 280 " model vdw 2.155 3.120 ... (remaining 163534 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 201 or resid 215 through 625 or resid 645 throug \ h 1402)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 6.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.150 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 0.006 0.121 19801 Z= 0.391 Angle : 0.810 10.398 26638 Z= 0.552 Chirality : 0.049 0.252 2886 Planarity : 0.009 0.234 3459 Dihedral : 16.688 89.181 7565 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.40 % Rotamer: Outliers : 0.48 % Allowed : 16.44 % Favored : 83.08 % 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: -0.42 (0.17), residues: 2388 helix: 0.72 (0.14), residues: 1355 sheet: -2.43 (0.43), residues: 139 loop : -1.42 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 453 TYR 0.014 0.001 TYR A 162 PHE 0.015 0.001 PHE E 34 TRP 0.010 0.001 TRP A 130 HIS 0.009 0.001 HIS B 753 Details of bonding type rmsd covalent geometry : bond 0.00569 (19800) covalent geometry : angle 0.81045 (26636) SS BOND : bond 0.00158 ( 1) SS BOND : angle 0.58307 ( 2) hydrogen bonds : bond 0.15669 ( 1089) hydrogen bonds : angle 6.40598 ( 3135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 308 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 807 ARG cc_start: 0.8243 (mmm-85) cc_final: 0.7909 (tpt170) REVERT: A 830 MET cc_start: 0.6916 (mmt) cc_final: 0.6399 (mmm) REVERT: A 865 LYS cc_start: 0.7843 (pttm) cc_final: 0.7593 (pttm) REVERT: D 74 ARG cc_start: 0.7497 (mtt180) cc_final: 0.7224 (mpt-90) outliers start: 10 outliers final: 2 residues processed: 315 average time/residue: 0.1569 time to fit residues: 75.3547 Evaluate side-chains 251 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 249 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain B residue 577 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN A 358 HIS A 581 HIS B 401 HIS B 479 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.182948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.143543 restraints weight = 32747.978| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.79 r_work: 0.3459 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 19801 Z= 0.291 Angle : 0.706 12.094 26638 Z= 0.358 Chirality : 0.044 0.172 2886 Planarity : 0.005 0.060 3459 Dihedral : 5.440 70.839 2607 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.25 % Allowed : 17.50 % Favored : 79.25 % 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: -0.25 (0.17), residues: 2388 helix: 0.89 (0.14), residues: 1347 sheet: -2.05 (0.42), residues: 134 loop : -1.44 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 51 TYR 0.017 0.002 TYR A 283 PHE 0.016 0.002 PHE D 53 TRP 0.010 0.002 TRP A 130 HIS 0.004 0.001 HIS B 753 Details of bonding type rmsd covalent geometry : bond 0.00683 (19800) covalent geometry : angle 0.70617 (26636) SS BOND : bond 0.00244 ( 1) SS BOND : angle 1.28618 ( 2) hydrogen bonds : bond 0.04938 ( 1089) hydrogen bonds : angle 5.03569 ( 3135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 260 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.7338 (mmm) cc_final: 0.7060 (mmm) REVERT: A 801 TYR cc_start: 0.7734 (t80) cc_final: 0.7501 (t80) REVERT: A 830 MET cc_start: 0.6881 (mmt) cc_final: 0.6322 (mmm) REVERT: B 439 MET cc_start: 0.7592 (tpp) cc_final: 0.7372 (tpp) REVERT: B 515 MET cc_start: 0.6145 (tpp) cc_final: 0.5835 (tpt) REVERT: C 53 PHE cc_start: 0.7379 (OUTLIER) cc_final: 0.6932 (t80) REVERT: D 74 ARG cc_start: 0.8333 (mtt180) cc_final: 0.7502 (mtt90) REVERT: F 161 THR cc_start: 0.8501 (p) cc_final: 0.8000 (t) outliers start: 68 outliers final: 41 residues processed: 303 average time/residue: 0.1362 time to fit residues: 64.9049 Evaluate side-chains 277 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 235 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 760 HIS Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 563 PHE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 120 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 210 optimal weight: 5.9990 chunk 1 optimal weight: 0.2980 chunk 78 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 179 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN C 68 GLN E 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.184030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.142285 restraints weight = 32984.133| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.65 r_work: 0.3488 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 19801 Z= 0.198 Angle : 0.625 12.468 26638 Z= 0.315 Chirality : 0.041 0.150 2886 Planarity : 0.004 0.060 3459 Dihedral : 5.252 73.347 2605 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.63 % Allowed : 17.64 % Favored : 78.73 % 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: -0.10 (0.17), residues: 2388 helix: 1.02 (0.14), residues: 1348 sheet: -2.02 (0.41), residues: 135 loop : -1.38 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 108 TYR 0.014 0.001 TYR A 310 PHE 0.023 0.002 PHE C 107 TRP 0.010 0.001 TRP B 438 HIS 0.003 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00459 (19800) covalent geometry : angle 0.62446 (26636) SS BOND : bond 0.00300 ( 1) SS BOND : angle 1.24044 ( 2) hydrogen bonds : bond 0.04362 ( 1089) hydrogen bonds : angle 4.71144 ( 3135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 259 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 807 ARG cc_start: 0.8382 (mmm-85) cc_final: 0.7990 (tpt170) REVERT: B 169 ARG cc_start: 0.7605 (mtm180) cc_final: 0.7388 (mtt90) REVERT: B 515 MET cc_start: 0.6103 (tpp) cc_final: 0.5743 (tpt) REVERT: B 903 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6344 (mm-30) REVERT: C 106 GLN cc_start: 0.6536 (mt0) cc_final: 0.6080 (mp10) REVERT: C 120 GLN cc_start: 0.7623 (mp10) cc_final: 0.7235 (mp10) REVERT: D 74 ARG cc_start: 0.8350 (mtt180) cc_final: 0.7372 (mtt90) REVERT: D 111 MET cc_start: 0.6575 (ppp) cc_final: 0.6328 (ppp) REVERT: D 133 PHE cc_start: 0.7198 (t80) cc_final: 0.6877 (t80) REVERT: E 30 PHE cc_start: 0.8001 (m-10) cc_final: 0.7737 (m-80) REVERT: E 107 LEU cc_start: 0.7651 (tt) cc_final: 0.7441 (mt) REVERT: F 161 THR cc_start: 0.8466 (p) cc_final: 0.7942 (t) outliers start: 76 outliers final: 42 residues processed: 309 average time/residue: 0.1348 time to fit residues: 66.2058 Evaluate side-chains 282 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 239 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 760 HIS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 563 PHE Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain F residue 40 ASN Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 124 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 78 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 98 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 228 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 26 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN C 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.185538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.148057 restraints weight = 33402.895| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.84 r_work: 0.3504 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19801 Z= 0.172 Angle : 0.606 13.004 26638 Z= 0.304 Chirality : 0.041 0.157 2886 Planarity : 0.004 0.057 3459 Dihedral : 5.170 74.756 2605 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.49 % Allowed : 19.07 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.17), residues: 2388 helix: 1.12 (0.14), residues: 1349 sheet: -1.98 (0.41), residues: 135 loop : -1.34 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 108 TYR 0.012 0.001 TYR A 310 PHE 0.028 0.002 PHE D 104 TRP 0.011 0.001 TRP B 438 HIS 0.004 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00396 (19800) covalent geometry : angle 0.60598 (26636) SS BOND : bond 0.00311 ( 1) SS BOND : angle 1.18387 ( 2) hydrogen bonds : bond 0.04055 ( 1089) hydrogen bonds : angle 4.54538 ( 3135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 256 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7316 (mp10) REVERT: A 807 ARG cc_start: 0.8259 (mmm-85) cc_final: 0.7996 (tpt90) REVERT: B 290 LEU cc_start: 0.5458 (OUTLIER) cc_final: 0.5196 (tp) REVERT: B 515 MET cc_start: 0.6169 (tpp) cc_final: 0.5762 (tpt) REVERT: B 903 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6352 (mm-30) REVERT: D 74 ARG cc_start: 0.8407 (mtt180) cc_final: 0.7401 (mtt90) REVERT: E 30 PHE cc_start: 0.7890 (m-10) cc_final: 0.7589 (m-80) REVERT: F 161 THR cc_start: 0.8489 (p) cc_final: 0.7996 (t) outliers start: 73 outliers final: 53 residues processed: 303 average time/residue: 0.1383 time to fit residues: 66.1008 Evaluate side-chains 298 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 242 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 760 HIS Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 563 PHE Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 837 LYS Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 120 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 92 optimal weight: 9.9990 chunk 64 optimal weight: 0.0770 chunk 121 optimal weight: 20.0000 chunk 217 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 HIS B 562 ASN C 68 GLN C 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.186303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.151479 restraints weight = 33223.509| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 2.73 r_work: 0.3548 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19801 Z= 0.153 Angle : 0.602 13.032 26638 Z= 0.298 Chirality : 0.040 0.198 2886 Planarity : 0.003 0.051 3459 Dihedral : 5.112 75.175 2605 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.92 % Allowed : 19.50 % Favored : 76.58 % 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: 0.13 (0.17), residues: 2388 helix: 1.20 (0.14), residues: 1349 sheet: -1.92 (0.41), residues: 135 loop : -1.28 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 108 TYR 0.012 0.001 TYR A 310 PHE 0.041 0.002 PHE F 54 TRP 0.013 0.001 TRP B 438 HIS 0.003 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00349 (19800) covalent geometry : angle 0.60191 (26636) SS BOND : bond 0.00319 ( 1) SS BOND : angle 1.15984 ( 2) hydrogen bonds : bond 0.03903 ( 1089) hydrogen bonds : angle 4.44157 ( 3135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 254 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7319 (mp10) REVERT: B 515 MET cc_start: 0.6137 (tpp) cc_final: 0.5719 (tpt) REVERT: B 903 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6377 (mm-30) REVERT: D 74 ARG cc_start: 0.8371 (mtt180) cc_final: 0.7605 (mpt-90) REVERT: D 110 MET cc_start: 0.6665 (tmm) cc_final: 0.6370 (ptm) REVERT: E 30 PHE cc_start: 0.7718 (m-10) cc_final: 0.7426 (m-80) REVERT: E 140 TRP cc_start: 0.5582 (OUTLIER) cc_final: 0.5119 (t-100) REVERT: F 87 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.6255 (t80) REVERT: F 161 THR cc_start: 0.8457 (p) cc_final: 0.7975 (t) outliers start: 82 outliers final: 58 residues processed: 305 average time/residue: 0.1381 time to fit residues: 66.2618 Evaluate side-chains 300 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 238 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 563 PHE Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 837 LYS Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 140 TRP Chi-restraints excluded: chain E residue 153 TYR Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 124 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 214 optimal weight: 0.8980 chunk 189 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 chunk 185 optimal weight: 0.0370 chunk 199 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 108 optimal weight: 3.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 HIS B 224 ASN C 68 GLN C 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.187411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.147611 restraints weight = 33165.463| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.50 r_work: 0.3549 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19801 Z= 0.120 Angle : 0.585 13.104 26638 Z= 0.289 Chirality : 0.040 0.181 2886 Planarity : 0.003 0.048 3459 Dihedral : 4.990 75.299 2605 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.30 % Allowed : 20.27 % Favored : 76.43 % 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: 0.35 (0.18), residues: 2388 helix: 1.35 (0.14), residues: 1353 sheet: -1.74 (0.42), residues: 135 loop : -1.17 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 807 TYR 0.011 0.001 TYR A 310 PHE 0.033 0.001 PHE C 107 TRP 0.015 0.001 TRP B 438 HIS 0.002 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00265 (19800) covalent geometry : angle 0.58522 (26636) SS BOND : bond 0.00346 ( 1) SS BOND : angle 1.18118 ( 2) hydrogen bonds : bond 0.03688 ( 1089) hydrogen bonds : angle 4.31152 ( 3135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 264 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7421 (mp10) REVERT: B 77 MET cc_start: 0.6160 (tpp) cc_final: 0.5929 (mtp) REVERT: B 93 LEU cc_start: 0.7378 (mm) cc_final: 0.6932 (tp) REVERT: B 290 LEU cc_start: 0.5186 (OUTLIER) cc_final: 0.4934 (tp) REVERT: B 515 MET cc_start: 0.6082 (tpp) cc_final: 0.5844 (tpp) REVERT: B 837 LYS cc_start: 0.6098 (OUTLIER) cc_final: 0.5282 (tttt) REVERT: B 903 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6383 (mm-30) REVERT: C 111 MET cc_start: 0.8029 (tmm) cc_final: 0.7719 (ttt) REVERT: D 74 ARG cc_start: 0.8399 (mtt180) cc_final: 0.7425 (mtt90) REVERT: D 110 MET cc_start: 0.6883 (tmm) cc_final: 0.6527 (ptm) REVERT: E 30 PHE cc_start: 0.8040 (m-10) cc_final: 0.7674 (m-80) REVERT: F 87 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.6445 (t80) REVERT: F 161 THR cc_start: 0.8539 (p) cc_final: 0.8059 (t) outliers start: 69 outliers final: 50 residues processed: 315 average time/residue: 0.1396 time to fit residues: 69.3337 Evaluate side-chains 295 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 240 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 837 LYS Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 TYR Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 124 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 141 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 212 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 164 optimal weight: 0.6980 chunk 207 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN C 106 GLN F 26 GLN F 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.186626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.152178 restraints weight = 33333.327| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.69 r_work: 0.3555 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19801 Z= 0.155 Angle : 0.617 13.363 26638 Z= 0.304 Chirality : 0.041 0.273 2886 Planarity : 0.003 0.052 3459 Dihedral : 5.026 73.943 2605 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.73 % Allowed : 20.60 % Favored : 75.67 % 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: 0.33 (0.17), residues: 2388 helix: 1.33 (0.14), residues: 1354 sheet: -1.80 (0.41), residues: 136 loop : -1.16 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 58 TYR 0.012 0.001 TYR A 310 PHE 0.022 0.001 PHE D 56 TRP 0.016 0.002 TRP B 438 HIS 0.003 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00355 (19800) covalent geometry : angle 0.61681 (26636) SS BOND : bond 0.00309 ( 1) SS BOND : angle 1.10766 ( 2) hydrogen bonds : bond 0.03782 ( 1089) hydrogen bonds : angle 4.32620 ( 3135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 252 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7415 (mp10) REVERT: B 93 LEU cc_start: 0.7383 (mm) cc_final: 0.6867 (tp) REVERT: B 290 LEU cc_start: 0.5670 (OUTLIER) cc_final: 0.5390 (tp) REVERT: B 515 MET cc_start: 0.6120 (tpp) cc_final: 0.5688 (tpt) REVERT: B 903 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6427 (mm-30) REVERT: C 106 GLN cc_start: 0.6446 (OUTLIER) cc_final: 0.6181 (mp10) REVERT: C 111 MET cc_start: 0.7904 (tmm) cc_final: 0.7693 (ttt) REVERT: D 110 MET cc_start: 0.6716 (tmm) cc_final: 0.6464 (ptm) REVERT: E 30 PHE cc_start: 0.7826 (m-10) cc_final: 0.7578 (m-80) REVERT: F 87 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.6339 (t80) REVERT: F 161 THR cc_start: 0.8482 (p) cc_final: 0.8024 (t) outliers start: 78 outliers final: 61 residues processed: 305 average time/residue: 0.1368 time to fit residues: 65.8714 Evaluate side-chains 306 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 240 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 837 LYS Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 TYR Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 40 ASN Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 124 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 151 optimal weight: 8.9990 chunk 208 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 222 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 228 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 HIS C 68 GLN E 118 GLN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.186575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.150768 restraints weight = 33413.854| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.63 r_work: 0.3532 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19801 Z= 0.156 Angle : 0.618 13.707 26638 Z= 0.304 Chirality : 0.041 0.225 2886 Planarity : 0.004 0.059 3459 Dihedral : 5.021 74.053 2605 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.68 % Allowed : 20.36 % Favored : 75.96 % 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: 0.34 (0.17), residues: 2388 helix: 1.34 (0.14), residues: 1354 sheet: -1.74 (0.41), residues: 136 loop : -1.16 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 807 TYR 0.012 0.001 TYR A 310 PHE 0.034 0.002 PHE D 104 TRP 0.017 0.002 TRP B 438 HIS 0.002 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00360 (19800) covalent geometry : angle 0.61769 (26636) SS BOND : bond 0.00307 ( 1) SS BOND : angle 1.09135 ( 2) hydrogen bonds : bond 0.03766 ( 1089) hydrogen bonds : angle 4.30341 ( 3135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 242 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7429 (mp10) REVERT: B 93 LEU cc_start: 0.7402 (mm) cc_final: 0.6876 (tp) REVERT: B 290 LEU cc_start: 0.5628 (OUTLIER) cc_final: 0.5349 (tp) REVERT: B 515 MET cc_start: 0.6057 (tpp) cc_final: 0.5639 (tpt) REVERT: B 903 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6420 (mm-30) REVERT: C 111 MET cc_start: 0.7933 (tmm) cc_final: 0.7725 (ttt) REVERT: D 110 MET cc_start: 0.6755 (tmm) cc_final: 0.6446 (ptm) REVERT: E 30 PHE cc_start: 0.7853 (m-10) cc_final: 0.7600 (m-80) REVERT: F 87 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.6480 (t80) REVERT: F 161 THR cc_start: 0.8505 (p) cc_final: 0.8052 (t) outliers start: 77 outliers final: 64 residues processed: 297 average time/residue: 0.1283 time to fit residues: 61.2431 Evaluate side-chains 307 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 239 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 760 HIS Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 563 PHE Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 837 LYS Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 TYR Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 40 ASN Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 124 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 78 optimal weight: 7.9990 chunk 91 optimal weight: 0.0870 chunk 123 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 162 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 overall best weight: 1.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 HIS B 224 ASN B 562 ASN C 68 GLN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.186856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.151946 restraints weight = 33129.448| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 2.60 r_work: 0.3565 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19801 Z= 0.141 Angle : 0.617 13.908 26638 Z= 0.302 Chirality : 0.040 0.265 2886 Planarity : 0.004 0.062 3459 Dihedral : 4.988 74.007 2605 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.54 % Allowed : 20.84 % Favored : 75.62 % 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: 0.39 (0.18), residues: 2388 helix: 1.38 (0.14), residues: 1355 sheet: -1.95 (0.38), residues: 153 loop : -1.07 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 41 TYR 0.022 0.001 TYR B 422 PHE 0.036 0.001 PHE B 46 TRP 0.019 0.002 TRP B 438 HIS 0.002 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00322 (19800) covalent geometry : angle 0.61682 (26636) SS BOND : bond 0.00314 ( 1) SS BOND : angle 1.11001 ( 2) hydrogen bonds : bond 0.03693 ( 1089) hydrogen bonds : angle 4.24273 ( 3135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 244 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7515 (mp10) REVERT: A 848 GLU cc_start: 0.7925 (pt0) cc_final: 0.7625 (pt0) REVERT: B 93 LEU cc_start: 0.7349 (mm) cc_final: 0.6806 (tp) REVERT: B 290 LEU cc_start: 0.5631 (OUTLIER) cc_final: 0.5349 (tp) REVERT: B 515 MET cc_start: 0.6024 (tpp) cc_final: 0.5625 (tpt) REVERT: B 903 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6436 (mm-30) REVERT: D 110 MET cc_start: 0.6735 (tmm) cc_final: 0.6412 (ptm) REVERT: E 30 PHE cc_start: 0.7840 (m-10) cc_final: 0.7575 (m-80) REVERT: F 87 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.6413 (t80) REVERT: F 161 THR cc_start: 0.8496 (p) cc_final: 0.8047 (t) outliers start: 74 outliers final: 63 residues processed: 295 average time/residue: 0.1344 time to fit residues: 63.1722 Evaluate side-chains 308 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 241 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 760 HIS Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 563 PHE Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 TYR Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 40 ASN Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 3 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 chunk 204 optimal weight: 0.0030 chunk 147 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 202 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 210 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 HIS ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.186833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.152366 restraints weight = 33343.124| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.64 r_work: 0.3557 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19801 Z= 0.146 Angle : 0.634 13.843 26638 Z= 0.310 Chirality : 0.041 0.304 2886 Planarity : 0.004 0.063 3459 Dihedral : 4.990 73.585 2605 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.49 % Allowed : 20.94 % Favored : 75.57 % 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: 0.43 (0.18), residues: 2388 helix: 1.41 (0.14), residues: 1350 sheet: -1.94 (0.38), residues: 153 loop : -1.03 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 807 TYR 0.022 0.001 TYR B 422 PHE 0.038 0.001 PHE D 104 TRP 0.020 0.002 TRP B 438 HIS 0.003 0.001 HIS D 148 Details of bonding type rmsd covalent geometry : bond 0.00336 (19800) covalent geometry : angle 0.63399 (26636) SS BOND : bond 0.00306 ( 1) SS BOND : angle 1.10724 ( 2) hydrogen bonds : bond 0.03700 ( 1089) hydrogen bonds : angle 4.24318 ( 3135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 244 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7544 (mp10) REVERT: A 848 GLU cc_start: 0.7966 (pt0) cc_final: 0.7679 (pt0) REVERT: B 93 LEU cc_start: 0.7386 (mm) cc_final: 0.6818 (tp) REVERT: B 290 LEU cc_start: 0.5614 (OUTLIER) cc_final: 0.5337 (tp) REVERT: B 515 MET cc_start: 0.6027 (tpp) cc_final: 0.5624 (tpt) REVERT: B 691 HIS cc_start: 0.8008 (t-170) cc_final: 0.7732 (t-170) REVERT: B 903 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6406 (mm-30) REVERT: D 110 MET cc_start: 0.6776 (tmm) cc_final: 0.6407 (ptm) REVERT: D 111 MET cc_start: 0.6994 (ppp) cc_final: 0.6635 (ppp) REVERT: F 87 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.6435 (t80) REVERT: F 161 THR cc_start: 0.8517 (p) cc_final: 0.8069 (t) outliers start: 73 outliers final: 64 residues processed: 295 average time/residue: 0.1325 time to fit residues: 62.1092 Evaluate side-chains 307 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 239 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 760 HIS Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 563 PHE Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 TYR Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 40 ASN Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 90 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 163 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 191 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 581 HIS ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN ** E 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.188203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.147376 restraints weight = 33078.032| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.74 r_work: 0.3534 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19801 Z= 0.133 Angle : 0.643 14.745 26638 Z= 0.314 Chirality : 0.041 0.284 2886 Planarity : 0.004 0.063 3459 Dihedral : 4.965 73.341 2605 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.39 % Allowed : 21.22 % Favored : 75.38 % 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: 0.46 (0.18), residues: 2388 helix: 1.43 (0.14), residues: 1353 sheet: -1.89 (0.39), residues: 153 loop : -1.03 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 807 TYR 0.023 0.001 TYR B 422 PHE 0.036 0.001 PHE B 46 TRP 0.021 0.001 TRP B 438 HIS 0.003 0.001 HIS D 148 Details of bonding type rmsd covalent geometry : bond 0.00301 (19800) covalent geometry : angle 0.64285 (26636) SS BOND : bond 0.00311 ( 1) SS BOND : angle 1.14059 ( 2) hydrogen bonds : bond 0.03674 ( 1089) hydrogen bonds : angle 4.21787 ( 3135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4979.48 seconds wall clock time: 86 minutes 7.21 seconds (5167.21 seconds total)