Starting phenix.real_space_refine on Wed Jan 14 01:09:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d7v_27235/01_2026/8d7v_27235.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d7v_27235/01_2026/8d7v_27235.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d7v_27235/01_2026/8d7v_27235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d7v_27235/01_2026/8d7v_27235.map" model { file = "/net/cci-nas-00/data/ceres_data/8d7v_27235/01_2026/8d7v_27235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d7v_27235/01_2026/8d7v_27235.cif" } 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= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 56 5.16 5 C 6906 2.51 5 N 1880 2.21 5 O 2071 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10915 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1127, 7902 Classifications: {'peptide': 1127} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 285} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 1086} Chain breaks: 2 Unresolved non-hydrogen bonds: 954 Unresolved non-hydrogen angles: 1214 Unresolved non-hydrogen dihedrals: 765 Unresolved non-hydrogen chiralities: 106 Planarities with less than four sites: {'GLU:plan': 25, 'ASP:plan': 17, 'ARG:plan': 16, 'GLN:plan1': 17, 'HIS:plan': 9, 'TRP:plan': 3, 'ASN:plan1': 14, 'PHE:plan': 7, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 497 Chain: "B" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2970 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 21, 'TRANS': 362} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 8, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {' ZN': 1, 'QFC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10096 SG CYS B 323 40.535 87.771 30.158 1.00359.10 S ATOM 10112 SG CYS B 326 39.439 91.345 29.399 1.00365.36 S ATOM 10610 SG CYS B 391 37.883 88.486 27.297 1.00400.95 S ATOM 10629 SG CYS B 394 41.427 89.606 26.957 1.00399.05 S Time building chain proxies: 2.43, per 1000 atoms: 0.22 Number of scatterers: 10915 At special positions: 0 Unit cell: (90.85, 110.4, 155.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 56 16.00 F 1 9.00 O 2071 8.00 N 1880 7.00 C 6906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.88 Conformation dependent library (CDL) restraints added in 369.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 394 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 326 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 323 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 391 " Number of angles added : 6 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2832 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 28 sheets defined 11.9% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 250 through 254 removed outlier: 3.788A pdb=" N ILE A 253 " --> pdb=" O PRO A 250 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 254 " --> pdb=" O PRO A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 254' Processing helix chain 'A' and resid 381 through 384 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 1044 through 1059 Processing helix chain 'A' and resid 1069 through 1075 Processing helix chain 'A' and resid 1091 through 1097 Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1101 through 1109 removed outlier: 3.535A pdb=" N VAL A1109 " --> pdb=" O MET A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1138 Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 57 through 61 removed outlier: 3.763A pdb=" N GLY B 61 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 148 through 152 Processing helix chain 'B' and resid 220 through 232 removed outlier: 3.702A pdb=" N GLN B 225 " --> pdb=" O TYR B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.650A pdb=" N ASN B 236 " --> pdb=" O HIS B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 removed outlier: 3.553A pdb=" N TYR B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 265 removed outlier: 3.613A pdb=" N LEU B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 288 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 303 through 318 Processing sheet with id=AA1, first strand: chain 'A' and resid 1004 through 1009 removed outlier: 3.623A pdb=" N VAL A1006 " --> pdb=" O GLY A1031 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLY A1026 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N SER A1042 " --> pdb=" O GLY A1026 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A1030 " --> pdb=" O GLY A1038 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 21 removed outlier: 6.591A pdb=" N LEU A 39 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU A 54 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE A 41 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 67 removed outlier: 3.862A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA A 86 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N HIS A 105 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 88 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124 removed outlier: 4.672A pdb=" N LEU A 135 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 169 removed outlier: 6.702A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N PHE A 169 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N THR A 177 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 218 through 221 Processing sheet with id=AA7, first strand: chain 'A' and resid 258 through 263 removed outlier: 6.890A pdb=" N GLY A 274 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS A 261 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU A 272 " --> pdb=" O HIS A 261 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ARG A 263 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ARG A 270 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP A 275 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU A 280 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 289 through 290 removed outlier: 4.066A pdb=" N GLU A 289 " --> pdb=" O THR A 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 313 removed outlier: 7.142A pdb=" N GLY A 325 " --> pdb=" O GLU A 312 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 311 through 313 removed outlier: 7.142A pdb=" N GLY A 325 " --> pdb=" O GLU A 312 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER A 331 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR A 352 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU A 333 " --> pdb=" O MET A 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 362 through 365 removed outlier: 3.602A pdb=" N ARG A 388 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 396 through 400 removed outlier: 4.902A pdb=" N GLU A 398 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR A 703 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 678 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 410 through 413 Processing sheet with id=AB5, first strand: chain 'A' and resid 467 through 471 removed outlier: 4.050A pdb=" N ARG A 477 " --> pdb=" O GLN A 470 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL A 476 " --> pdb=" O GLU A 489 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLU A 489 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU A 478 " --> pdb=" O VAL A 487 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 500 through 503 removed outlier: 3.528A pdb=" N VAL A 500 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A 516 " --> pdb=" O HIS A 531 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N HIS A 531 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR A 518 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.526A pdb=" N GLY A 559 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU A 541 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA A 557 " --> pdb=" O LEU A 541 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 565 through 569 removed outlier: 6.867A pdb=" N ALA A 566 " --> pdb=" O LYS A 579 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS A 579 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE A 568 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 588 through 594 removed outlier: 4.256A pdb=" N ALA A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 613 " --> pdb=" O LYS A 627 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A 627 " --> pdb=" O TYR A 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 637 through 639 removed outlier: 3.749A pdb=" N CYS A 652 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.873A pdb=" N SER A 738 " --> pdb=" O PRO A 721 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS A 723 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP A 795 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 801 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N SER A 762 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N GLN A 806 " --> pdb=" O SER A 762 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER A 764 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 811 through 819 removed outlier: 6.766A pdb=" N GLY A 832 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU A 816 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE A 830 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER A 818 " --> pdb=" O TYR A 828 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TYR A 828 " --> pdb=" O SER A 818 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 847 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLN A 852 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N THR A 860 " --> pdb=" O GLN A 852 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N SER A 854 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LEU A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 870 through 875 removed outlier: 4.331A pdb=" N SER A 872 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL A 888 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN A 904 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 890 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 913 through 916 removed outlier: 7.081A pdb=" N VAL A 930 " --> pdb=" O ARG A 947 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ARG A 947 " --> pdb=" O VAL A 930 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU A 932 " --> pdb=" O ILE A 945 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A 941 " --> pdb=" O LYS A 936 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 954 through 959 removed outlier: 3.665A pdb=" N ALA A 956 " --> pdb=" O ALA A 968 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU A 974 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU A 997 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL A 976 " --> pdb=" O VAL A 995 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 65 through 66 removed outlier: 8.177A pdb=" N GLN B 134 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS B 166 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLY B 136 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ARG B 164 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR B 138 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS B 158 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR B 144 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS B 156 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 78 through 82 removed outlier: 6.844A pdb=" N LYS B 156 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR B 144 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS B 158 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR B 138 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ARG B 164 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLY B 136 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS B 166 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N GLN B 134 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE B 135 " --> pdb=" O ALA B 124 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AD1, first strand: chain 'B' and resid 346 through 350 removed outlier: 7.572A pdb=" N HIS B 397 " --> pdb=" O CYS B 391 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N CYS B 391 " --> pdb=" O HIS B 397 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY B 399 " --> pdb=" O ALA B 389 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1884 1.28 - 1.41: 2649 1.41 - 1.54: 6492 1.54 - 1.68: 18 1.68 - 1.81: 82 Bond restraints: 11125 Sorted by residual: bond pdb=" N QFC B 502 " pdb=" C5 QFC B 502 " ideal model delta sigma weight residual 1.372 1.411 -0.039 2.00e-02 2.50e+03 3.81e+00 bond pdb=" N LEU B 202 " pdb=" CA LEU B 202 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.71e+00 bond pdb=" CG PRO B 85 " pdb=" CD PRO B 85 " ideal model delta sigma weight residual 1.503 1.562 -0.059 3.40e-02 8.65e+02 3.04e+00 bond pdb=" CB PRO B 85 " pdb=" CG PRO B 85 " ideal model delta sigma weight residual 1.492 1.567 -0.075 5.00e-02 4.00e+02 2.26e+00 bond pdb=" CA GLY A 832 " pdb=" C GLY A 832 " ideal model delta sigma weight residual 1.520 1.510 0.010 7.30e-03 1.88e+04 1.77e+00 ... (remaining 11120 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 14728 1.69 - 3.37: 380 3.37 - 5.06: 56 5.06 - 6.74: 10 6.74 - 8.43: 5 Bond angle restraints: 15179 Sorted by residual: angle pdb=" N PRO B 98 " pdb=" CA PRO B 98 " pdb=" CB PRO B 98 " ideal model delta sigma weight residual 103.23 110.19 -6.96 1.13e+00 7.83e-01 3.80e+01 angle pdb=" CA PRO B 85 " pdb=" N PRO B 85 " pdb=" CD PRO B 85 " ideal model delta sigma weight residual 112.00 107.60 4.40 1.40e+00 5.10e-01 9.90e+00 angle pdb=" N VAL A 52 " pdb=" CA VAL A 52 " pdb=" C VAL A 52 " ideal model delta sigma weight residual 111.62 109.21 2.41 7.90e-01 1.60e+00 9.30e+00 angle pdb=" C GLU A1123 " pdb=" N ALA A1124 " pdb=" CA ALA A1124 " ideal model delta sigma weight residual 121.54 126.74 -5.20 1.91e+00 2.74e-01 7.40e+00 angle pdb=" O SER B 201 " pdb=" C SER B 201 " pdb=" N LEU B 202 " ideal model delta sigma weight residual 122.19 125.37 -3.18 1.18e+00 7.18e-01 7.26e+00 ... (remaining 15174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6058 17.96 - 35.92: 478 35.92 - 53.88: 82 53.88 - 71.84: 20 71.84 - 89.80: 14 Dihedral angle restraints: 6652 sinusoidal: 2271 harmonic: 4381 Sorted by residual: dihedral pdb=" CA LYS B 181 " pdb=" C LYS B 181 " pdb=" N VAL B 182 " pdb=" CA VAL B 182 " ideal model delta harmonic sigma weight residual -180.00 -157.81 -22.19 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA GLU A 969 " pdb=" C GLU A 969 " pdb=" N ASN A 970 " pdb=" CA ASN A 970 " ideal model delta harmonic sigma weight residual 180.00 -161.58 -18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA SER B 201 " pdb=" C SER B 201 " pdb=" N LEU B 202 " pdb=" CA LEU B 202 " ideal model delta harmonic sigma weight residual 180.00 162.28 17.72 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 6649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1106 0.037 - 0.075: 456 0.075 - 0.112: 162 0.112 - 0.150: 44 0.150 - 0.187: 4 Chirality restraints: 1772 Sorted by residual: chirality pdb=" CG LEU B 253 " pdb=" CB LEU B 253 " pdb=" CD1 LEU B 253 " pdb=" CD2 LEU B 253 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CA PRO B 98 " pdb=" N PRO B 98 " pdb=" C PRO B 98 " pdb=" CB PRO B 98 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CB VAL B 197 " pdb=" CA VAL B 197 " pdb=" CG1 VAL B 197 " pdb=" CG2 VAL B 197 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 1769 not shown) Planarity restraints: 1992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" O QFC B 502 " 0.024 2.00e-02 2.50e+03 2.70e-02 2.18e+01 pdb=" C14 QFC B 502 " -0.002 2.00e-02 2.50e+03 pdb=" C15 QFC B 502 " -0.026 2.00e-02 2.50e+03 pdb=" C16 QFC B 502 " -0.028 2.00e-02 2.50e+03 pdb=" C17 QFC B 502 " -0.006 2.00e-02 2.50e+03 pdb=" C18 QFC B 502 " 0.013 2.00e-02 2.50e+03 pdb=" C19 QFC B 502 " 0.022 2.00e-02 2.50e+03 pdb=" C20 QFC B 502 " 0.015 2.00e-02 2.50e+03 pdb=" C21 QFC B 502 " 0.013 2.00e-02 2.50e+03 pdb=" C22 QFC B 502 " -0.067 2.00e-02 2.50e+03 pdb=" N2 QFC B 502 " 0.010 2.00e-02 2.50e+03 pdb=" O1 QFC B 502 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 423 " -0.068 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO B 424 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO B 424 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 424 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 288 " -0.059 5.00e-02 4.00e+02 9.10e-02 1.32e+01 pdb=" N PRO B 289 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO B 289 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 289 " -0.049 5.00e-02 4.00e+02 ... (remaining 1989 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 798 2.74 - 3.28: 10409 3.28 - 3.82: 17024 3.82 - 4.36: 20147 4.36 - 4.90: 36601 Nonbonded interactions: 84979 Sorted by model distance: nonbonded pdb=" O SER A1071 " pdb=" OG SER A1075 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASP B 149 " pdb=" N PHE B 150 " model vdw 2.215 3.120 nonbonded pdb=" OE2 GLU B 187 " pdb=" OH TYR B 282 " model vdw 2.231 3.040 nonbonded pdb=" ND2 ASN A 392 " pdb=" O LEU A1012 " model vdw 2.259 3.120 nonbonded pdb=" OG SER B 320 " pdb=" OG1 THR B 425 " model vdw 2.266 3.040 ... (remaining 84974 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.590 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 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 : 0.004 0.075 11129 Z= 0.191 Angle : 0.682 8.430 15185 Z= 0.363 Chirality : 0.047 0.187 1772 Planarity : 0.006 0.102 1992 Dihedral : 14.304 89.802 3820 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.66 % Favored : 93.95 % Rotamer: Outliers : 0.10 % Allowed : 0.20 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.21), residues: 1503 helix: -0.18 (0.39), residues: 171 sheet: -0.55 (0.23), residues: 548 loop : -1.86 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 171 TYR 0.016 0.002 TYR A 891 PHE 0.027 0.002 PHE B 165 TRP 0.059 0.003 TRP B 380 HIS 0.006 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00445 (11125) covalent geometry : angle 0.67556 (15179) hydrogen bonds : bond 0.14772 ( 381) hydrogen bonds : angle 7.62047 ( 1044) metal coordination : bond 0.00743 ( 4) metal coordination : angle 4.56918 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 TYR cc_start: 0.7640 (m-80) cc_final: 0.7429 (m-80) REVERT: A 74 LYS cc_start: 0.7979 (pttm) cc_final: 0.7711 (pttp) REVERT: A 892 GLU cc_start: 0.7550 (mt-10) cc_final: 0.6945 (mt-10) REVERT: A 963 ASP cc_start: 0.8167 (m-30) cc_final: 0.7853 (m-30) REVERT: A 969 GLU cc_start: 0.7823 (pt0) cc_final: 0.7597 (pt0) REVERT: A 1014 MET cc_start: 0.7191 (tpt) cc_final: 0.6830 (tpt) REVERT: B 50 ASP cc_start: 0.7491 (t70) cc_final: 0.7046 (t0) REVERT: B 89 MET cc_start: 0.7574 (ppp) cc_final: 0.7047 (ppp) REVERT: B 106 GLU cc_start: 0.7932 (mt-10) cc_final: 0.6849 (mp0) REVERT: B 294 LEU cc_start: 0.8243 (mt) cc_final: 0.7931 (mt) outliers start: 1 outliers final: 0 residues processed: 171 average time/residue: 0.1003 time to fit residues: 24.3034 Evaluate side-chains 130 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 GLN A 796 GLN A1140 HIS B 276 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.164798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.122408 restraints weight = 15786.291| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.41 r_work: 0.3363 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11129 Z= 0.131 Angle : 0.564 6.049 15185 Z= 0.298 Chirality : 0.045 0.194 1772 Planarity : 0.004 0.072 1992 Dihedral : 5.678 59.973 1636 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.92 % Favored : 94.68 % Rotamer: Outliers : 0.79 % Allowed : 9.05 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.21), residues: 1503 helix: -0.16 (0.39), residues: 173 sheet: -0.50 (0.23), residues: 534 loop : -1.73 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 111 TYR 0.021 0.001 TYR B 59 PHE 0.015 0.002 PHE A1097 TRP 0.020 0.002 TRP B 380 HIS 0.004 0.001 HIS A1140 Details of bonding type rmsd covalent geometry : bond 0.00300 (11125) covalent geometry : angle 0.56035 (15179) hydrogen bonds : bond 0.03615 ( 381) hydrogen bonds : angle 6.01355 ( 1044) metal coordination : bond 0.00546 ( 4) metal coordination : angle 3.25382 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 SER cc_start: 0.8417 (m) cc_final: 0.7931 (p) REVERT: A 835 MET cc_start: 0.8445 (mmm) cc_final: 0.8150 (mtt) REVERT: A 987 GLU cc_start: 0.7985 (pm20) cc_final: 0.7394 (tp30) REVERT: A 1014 MET cc_start: 0.7707 (tpt) cc_final: 0.7382 (tpt) REVERT: B 50 ASP cc_start: 0.7820 (t70) cc_final: 0.7242 (t0) REVERT: B 74 ASP cc_start: 0.7741 (p0) cc_final: 0.7499 (p0) REVERT: B 89 MET cc_start: 0.7777 (ppp) cc_final: 0.7402 (ppp) REVERT: B 140 GLU cc_start: 0.4773 (tm-30) cc_final: 0.4479 (tm-30) REVERT: B 200 GLU cc_start: 0.8137 (mp0) cc_final: 0.7728 (mp0) REVERT: B 263 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7174 (mm-30) REVERT: B 294 LEU cc_start: 0.8560 (mt) cc_final: 0.8244 (mt) REVERT: B 331 ILE cc_start: 0.7636 (mp) cc_final: 0.6938 (tt) outliers start: 8 outliers final: 5 residues processed: 153 average time/residue: 0.0976 time to fit residues: 21.4870 Evaluate side-chains 133 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 296 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 100 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 51 optimal weight: 40.0000 chunk 57 optimal weight: 0.0770 chunk 94 optimal weight: 0.9990 chunk 123 optimal weight: 0.0000 chunk 92 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.0148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1140 HIS B 112 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.164323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.118514 restraints weight = 16012.116| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.09 r_work: 0.3362 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11129 Z= 0.129 Angle : 0.527 5.319 15185 Z= 0.277 Chirality : 0.044 0.179 1772 Planarity : 0.004 0.063 1992 Dihedral : 5.192 49.419 1636 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.59 % Favored : 94.15 % Rotamer: Outliers : 1.28 % Allowed : 11.60 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.21), residues: 1503 helix: -0.12 (0.39), residues: 173 sheet: -0.40 (0.23), residues: 533 loop : -1.77 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 111 TYR 0.013 0.001 TYR B 142 PHE 0.016 0.002 PHE A 851 TRP 0.014 0.002 TRP A 207 HIS 0.005 0.001 HIS A1140 Details of bonding type rmsd covalent geometry : bond 0.00304 (11125) covalent geometry : angle 0.52327 (15179) hydrogen bonds : bond 0.03356 ( 381) hydrogen bonds : angle 5.50912 ( 1044) metal coordination : bond 0.00512 ( 4) metal coordination : angle 3.02660 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 SER cc_start: 0.8397 (m) cc_final: 0.7894 (p) REVERT: A 835 MET cc_start: 0.8437 (mmm) cc_final: 0.8233 (mmm) REVERT: A 1014 MET cc_start: 0.7629 (tpt) cc_final: 0.7317 (tpt) REVERT: B 50 ASP cc_start: 0.7844 (t70) cc_final: 0.7233 (t0) REVERT: B 89 MET cc_start: 0.7770 (ppp) cc_final: 0.7282 (ppp) REVERT: B 145 ARG cc_start: 0.8007 (tpp80) cc_final: 0.7464 (mtm-85) REVERT: B 294 LEU cc_start: 0.8568 (mt) cc_final: 0.8270 (mt) REVERT: B 331 ILE cc_start: 0.7621 (mp) cc_final: 0.6867 (tt) REVERT: B 349 TYR cc_start: 0.4411 (m-80) cc_final: 0.3987 (m-80) outliers start: 13 outliers final: 8 residues processed: 150 average time/residue: 0.0866 time to fit residues: 19.7984 Evaluate side-chains 130 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 362 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 79 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 114 optimal weight: 40.0000 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 59 optimal weight: 40.0000 chunk 102 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 148 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 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 374 GLN A 731 GLN A 796 GLN A 797 HIS A1140 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.159156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.116947 restraints weight = 16011.232| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.48 r_work: 0.3236 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 11129 Z= 0.280 Angle : 0.641 6.691 15185 Z= 0.334 Chirality : 0.047 0.165 1772 Planarity : 0.005 0.060 1992 Dihedral : 5.501 50.185 1636 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.79 % Favored : 92.95 % Rotamer: Outliers : 1.67 % Allowed : 13.47 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.21), residues: 1503 helix: -0.57 (0.37), residues: 172 sheet: -0.54 (0.23), residues: 541 loop : -1.95 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 111 TYR 0.018 0.002 TYR A 91 PHE 0.021 0.003 PHE A 23 TRP 0.014 0.002 TRP A 207 HIS 0.005 0.001 HIS A1140 Details of bonding type rmsd covalent geometry : bond 0.00662 (11125) covalent geometry : angle 0.63846 (15179) hydrogen bonds : bond 0.03896 ( 381) hydrogen bonds : angle 5.77414 ( 1044) metal coordination : bond 0.00527 ( 4) metal coordination : angle 3.13474 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 TRP cc_start: 0.8550 (OUTLIER) cc_final: 0.6720 (p-90) REVERT: A 217 SER cc_start: 0.8765 (m) cc_final: 0.8218 (p) REVERT: A 835 MET cc_start: 0.8586 (mmm) cc_final: 0.8242 (mtt) REVERT: A 987 GLU cc_start: 0.8031 (pm20) cc_final: 0.7540 (tp30) REVERT: A 1025 GLN cc_start: 0.7338 (mp10) cc_final: 0.7101 (pp30) REVERT: B 50 ASP cc_start: 0.7875 (t70) cc_final: 0.7469 (t70) REVERT: B 89 MET cc_start: 0.7648 (ppp) cc_final: 0.7394 (ppp) REVERT: B 140 GLU cc_start: 0.4888 (tm-30) cc_final: 0.4669 (tm-30) REVERT: B 265 ASP cc_start: 0.6371 (OUTLIER) cc_final: 0.5329 (t0) REVERT: B 294 LEU cc_start: 0.8664 (mt) cc_final: 0.8274 (mt) REVERT: B 331 ILE cc_start: 0.7953 (mp) cc_final: 0.7103 (tt) outliers start: 17 outliers final: 12 residues processed: 132 average time/residue: 0.0935 time to fit residues: 18.2865 Evaluate side-chains 129 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 355 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 112 optimal weight: 0.0980 chunk 120 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 137 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1140 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.161696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.115326 restraints weight = 15682.047| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.53 r_work: 0.3296 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11129 Z= 0.130 Angle : 0.514 5.106 15185 Z= 0.272 Chirality : 0.044 0.147 1772 Planarity : 0.004 0.054 1992 Dihedral : 4.926 39.630 1636 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.32 % Favored : 94.41 % Rotamer: Outliers : 1.47 % Allowed : 15.63 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.21), residues: 1503 helix: -0.32 (0.39), residues: 174 sheet: -0.49 (0.23), residues: 527 loop : -1.83 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 369 TYR 0.011 0.001 TYR A 91 PHE 0.017 0.002 PHE A1097 TRP 0.016 0.002 TRP A 207 HIS 0.006 0.001 HIS A1140 Details of bonding type rmsd covalent geometry : bond 0.00304 (11125) covalent geometry : angle 0.51177 (15179) hydrogen bonds : bond 0.03048 ( 381) hydrogen bonds : angle 5.26992 ( 1044) metal coordination : bond 0.00393 ( 4) metal coordination : angle 2.33204 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 207 TRP cc_start: 0.8450 (OUTLIER) cc_final: 0.6589 (p-90) REVERT: A 217 SER cc_start: 0.8463 (m) cc_final: 0.7986 (p) REVERT: A 835 MET cc_start: 0.8482 (mmm) cc_final: 0.8166 (mmt) REVERT: A 987 GLU cc_start: 0.7993 (pm20) cc_final: 0.7517 (tp30) REVERT: B 89 MET cc_start: 0.7628 (ppp) cc_final: 0.7404 (ppp) REVERT: B 294 LEU cc_start: 0.8643 (mt) cc_final: 0.8303 (mt) REVERT: B 331 ILE cc_start: 0.7966 (mp) cc_final: 0.7122 (tt) REVERT: B 346 MET cc_start: 0.6424 (mmm) cc_final: 0.5890 (mmm) outliers start: 15 outliers final: 12 residues processed: 140 average time/residue: 0.0881 time to fit residues: 18.4678 Evaluate side-chains 133 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 409 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 3 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 148 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 46 optimal weight: 40.0000 chunk 37 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 797 HIS A1140 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.159101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.116650 restraints weight = 15860.367| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.31 r_work: 0.3232 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11129 Z= 0.232 Angle : 0.592 5.648 15185 Z= 0.310 Chirality : 0.046 0.143 1772 Planarity : 0.004 0.054 1992 Dihedral : 5.068 39.017 1636 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.92 % Favored : 92.81 % Rotamer: Outliers : 2.36 % Allowed : 15.54 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.21), residues: 1503 helix: -0.50 (0.38), residues: 175 sheet: -0.59 (0.22), residues: 545 loop : -1.95 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 111 TYR 0.018 0.002 TYR B 355 PHE 0.020 0.002 PHE A1097 TRP 0.015 0.002 TRP B 224 HIS 0.006 0.001 HIS A1140 Details of bonding type rmsd covalent geometry : bond 0.00550 (11125) covalent geometry : angle 0.58916 (15179) hydrogen bonds : bond 0.03553 ( 381) hydrogen bonds : angle 5.44626 ( 1044) metal coordination : bond 0.00450 ( 4) metal coordination : angle 2.77109 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.436 Fit side-chains REVERT: A 207 TRP cc_start: 0.8580 (OUTLIER) cc_final: 0.6862 (p-90) REVERT: A 217 SER cc_start: 0.8561 (m) cc_final: 0.8087 (p) REVERT: A 835 MET cc_start: 0.8616 (mmm) cc_final: 0.8049 (mtt) REVERT: A 910 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7439 (mtp) REVERT: A 987 GLU cc_start: 0.8033 (pm20) cc_final: 0.7568 (tp30) REVERT: B 50 ASP cc_start: 0.7736 (t0) cc_final: 0.7298 (t70) REVERT: B 158 LYS cc_start: 0.7935 (mmmt) cc_final: 0.7720 (ttmt) REVERT: B 265 ASP cc_start: 0.6115 (OUTLIER) cc_final: 0.5567 (t0) REVERT: B 294 LEU cc_start: 0.8624 (mt) cc_final: 0.8181 (mt) REVERT: B 346 MET cc_start: 0.6587 (mmm) cc_final: 0.6107 (mmm) outliers start: 24 outliers final: 18 residues processed: 137 average time/residue: 0.0809 time to fit residues: 17.2892 Evaluate side-chains 135 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1132 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 355 TYR Chi-restraints excluded: chain B residue 409 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 2 optimal weight: 2.9990 chunk 46 optimal weight: 30.0000 chunk 84 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 797 HIS A1140 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.160933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.118728 restraints weight = 15795.930| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.24 r_work: 0.3268 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11129 Z= 0.141 Angle : 0.533 6.353 15185 Z= 0.281 Chirality : 0.044 0.139 1772 Planarity : 0.004 0.052 1992 Dihedral : 4.766 33.376 1636 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.66 % Favored : 94.08 % Rotamer: Outliers : 2.75 % Allowed : 16.03 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.21), residues: 1503 helix: -0.18 (0.40), residues: 170 sheet: -0.60 (0.22), residues: 529 loop : -1.86 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 111 TYR 0.016 0.001 TYR B 355 PHE 0.018 0.002 PHE A1097 TRP 0.015 0.002 TRP A 207 HIS 0.006 0.001 HIS A1140 Details of bonding type rmsd covalent geometry : bond 0.00332 (11125) covalent geometry : angle 0.53143 (15179) hydrogen bonds : bond 0.03074 ( 381) hydrogen bonds : angle 5.18915 ( 1044) metal coordination : bond 0.00427 ( 4) metal coordination : angle 2.34291 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.412 Fit side-chains REVERT: A 207 TRP cc_start: 0.8528 (OUTLIER) cc_final: 0.6735 (p-90) REVERT: A 217 SER cc_start: 0.8486 (m) cc_final: 0.8032 (p) REVERT: A 835 MET cc_start: 0.8619 (mmm) cc_final: 0.8270 (mmt) REVERT: A 987 GLU cc_start: 0.7944 (pm20) cc_final: 0.7513 (tp30) REVERT: B 50 ASP cc_start: 0.7759 (t0) cc_final: 0.7406 (t70) REVERT: B 265 ASP cc_start: 0.6140 (OUTLIER) cc_final: 0.5582 (t0) REVERT: B 346 MET cc_start: 0.6642 (mmm) cc_final: 0.6110 (mmm) outliers start: 28 outliers final: 17 residues processed: 144 average time/residue: 0.0775 time to fit residues: 17.5280 Evaluate side-chains 135 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1132 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 409 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 35 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 51 optimal weight: 50.0000 chunk 134 optimal weight: 10.0000 chunk 88 optimal weight: 0.3980 chunk 117 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 797 HIS A1140 HIS B 115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.161306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.112196 restraints weight = 15796.651| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.86 r_work: 0.3306 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11129 Z= 0.132 Angle : 0.528 5.613 15185 Z= 0.280 Chirality : 0.045 0.140 1772 Planarity : 0.004 0.049 1992 Dihedral : 4.565 28.886 1636 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.99 % Favored : 93.75 % Rotamer: Outliers : 2.46 % Allowed : 16.72 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.21), residues: 1503 helix: -0.19 (0.39), residues: 171 sheet: -0.65 (0.22), residues: 547 loop : -1.79 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 111 TYR 0.018 0.001 TYR A1114 PHE 0.016 0.002 PHE A1097 TRP 0.015 0.001 TRP A 207 HIS 0.006 0.001 HIS A1140 Details of bonding type rmsd covalent geometry : bond 0.00310 (11125) covalent geometry : angle 0.52665 (15179) hydrogen bonds : bond 0.02988 ( 381) hydrogen bonds : angle 5.06866 ( 1044) metal coordination : bond 0.00349 ( 4) metal coordination : angle 2.03147 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.339 Fit side-chains REVERT: A 207 TRP cc_start: 0.8468 (OUTLIER) cc_final: 0.6644 (p-90) REVERT: A 217 SER cc_start: 0.8469 (m) cc_final: 0.8017 (p) REVERT: A 835 MET cc_start: 0.8530 (mmm) cc_final: 0.8162 (mmt) REVERT: A 987 GLU cc_start: 0.7987 (pm20) cc_final: 0.7555 (tp30) REVERT: B 50 ASP cc_start: 0.7658 (t0) cc_final: 0.7432 (t70) REVERT: B 140 GLU cc_start: 0.4580 (tm-30) cc_final: 0.4372 (tm-30) REVERT: B 144 TYR cc_start: 0.7701 (t80) cc_final: 0.7435 (t80) REVERT: B 265 ASP cc_start: 0.6146 (OUTLIER) cc_final: 0.5450 (t0) REVERT: B 346 MET cc_start: 0.6656 (mmm) cc_final: 0.6028 (mmm) outliers start: 25 outliers final: 20 residues processed: 140 average time/residue: 0.0843 time to fit residues: 18.2123 Evaluate side-chains 139 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1132 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 409 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 105 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 53 optimal weight: 30.0000 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 116 optimal weight: 0.0030 chunk 147 optimal weight: 9.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 797 HIS A1140 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.161129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.119621 restraints weight = 15667.661| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 3.49 r_work: 0.3258 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11129 Z= 0.154 Angle : 0.555 6.145 15185 Z= 0.293 Chirality : 0.045 0.163 1772 Planarity : 0.004 0.076 1992 Dihedral : 4.546 26.590 1636 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.19 % Favored : 93.55 % Rotamer: Outliers : 2.56 % Allowed : 16.91 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.21), residues: 1503 helix: -0.13 (0.40), residues: 170 sheet: -0.62 (0.22), residues: 545 loop : -1.80 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 111 TYR 0.013 0.001 TYR B 355 PHE 0.023 0.002 PHE B 135 TRP 0.014 0.001 TRP A 207 HIS 0.010 0.001 HIS A1140 Details of bonding type rmsd covalent geometry : bond 0.00363 (11125) covalent geometry : angle 0.55350 (15179) hydrogen bonds : bond 0.03168 ( 381) hydrogen bonds : angle 5.12751 ( 1044) metal coordination : bond 0.00371 ( 4) metal coordination : angle 2.26648 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.284 Fit side-chains REVERT: A 207 TRP cc_start: 0.8480 (OUTLIER) cc_final: 0.6650 (p-90) REVERT: A 217 SER cc_start: 0.8508 (m) cc_final: 0.8051 (p) REVERT: A 835 MET cc_start: 0.8613 (mmm) cc_final: 0.8247 (mmt) REVERT: A 987 GLU cc_start: 0.7942 (pm20) cc_final: 0.7573 (tp30) REVERT: B 50 ASP cc_start: 0.7654 (t0) cc_final: 0.7433 (t70) REVERT: B 140 GLU cc_start: 0.4712 (tm-30) cc_final: 0.4479 (tm-30) REVERT: B 265 ASP cc_start: 0.6339 (OUTLIER) cc_final: 0.5667 (t0) REVERT: B 346 MET cc_start: 0.6559 (mmm) cc_final: 0.6038 (mmm) outliers start: 26 outliers final: 20 residues processed: 134 average time/residue: 0.0776 time to fit residues: 16.4652 Evaluate side-chains 138 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1132 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 409 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 40.0000 chunk 11 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 61 optimal weight: 40.0000 chunk 70 optimal weight: 3.9990 chunk 85 optimal weight: 0.0170 chunk 109 optimal weight: 0.0770 chunk 138 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 overall best weight: 0.9178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 797 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.162358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.119743 restraints weight = 15705.972| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.16 r_work: 0.3289 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11129 Z= 0.119 Angle : 0.528 6.298 15185 Z= 0.280 Chirality : 0.044 0.153 1772 Planarity : 0.004 0.052 1992 Dihedral : 4.328 22.989 1636 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.85 % Favored : 93.95 % Rotamer: Outliers : 1.87 % Allowed : 18.09 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.21), residues: 1503 helix: -0.04 (0.41), residues: 171 sheet: -0.58 (0.22), residues: 549 loop : -1.79 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 419 TYR 0.021 0.001 TYR A1114 PHE 0.024 0.002 PHE B 135 TRP 0.015 0.001 TRP A 207 HIS 0.012 0.001 HIS A1140 Details of bonding type rmsd covalent geometry : bond 0.00279 (11125) covalent geometry : angle 0.52614 (15179) hydrogen bonds : bond 0.02906 ( 381) hydrogen bonds : angle 4.95487 ( 1044) metal coordination : bond 0.00360 ( 4) metal coordination : angle 2.00009 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.415 Fit side-chains REVERT: A 207 TRP cc_start: 0.8446 (OUTLIER) cc_final: 0.6580 (p-90) REVERT: A 217 SER cc_start: 0.8476 (m) cc_final: 0.8039 (p) REVERT: A 835 MET cc_start: 0.8565 (mmm) cc_final: 0.8169 (mmt) REVERT: A 987 GLU cc_start: 0.7915 (pm20) cc_final: 0.7573 (tp30) REVERT: A 1105 MET cc_start: 0.8251 (tpp) cc_final: 0.8006 (mmm) REVERT: B 50 ASP cc_start: 0.7608 (t0) cc_final: 0.7406 (t70) REVERT: B 140 GLU cc_start: 0.4766 (tm-30) cc_final: 0.4549 (tm-30) REVERT: B 265 ASP cc_start: 0.6557 (OUTLIER) cc_final: 0.6285 (t0) REVERT: B 346 MET cc_start: 0.6673 (mmm) cc_final: 0.6143 (mmm) outliers start: 19 outliers final: 16 residues processed: 135 average time/residue: 0.0800 time to fit residues: 16.9585 Evaluate side-chains 134 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 207 TRP Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1132 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 296 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 53 optimal weight: 30.0000 chunk 59 optimal weight: 40.0000 chunk 69 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 40 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 797 HIS A1140 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.159150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.112011 restraints weight = 15791.336| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.21 r_work: 0.3235 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11129 Z= 0.217 Angle : 0.601 6.821 15185 Z= 0.314 Chirality : 0.046 0.144 1772 Planarity : 0.004 0.051 1992 Dihedral : 4.550 22.407 1636 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.12 % Favored : 92.68 % Rotamer: Outliers : 2.26 % Allowed : 17.90 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.21), residues: 1503 helix: -0.19 (0.39), residues: 170 sheet: -0.66 (0.22), residues: 567 loop : -1.94 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 419 TYR 0.019 0.002 TYR A1114 PHE 0.029 0.002 PHE B 208 TRP 0.014 0.002 TRP B 224 HIS 0.011 0.001 HIS A1140 Details of bonding type rmsd covalent geometry : bond 0.00513 (11125) covalent geometry : angle 0.59864 (15179) hydrogen bonds : bond 0.03398 ( 381) hydrogen bonds : angle 5.26789 ( 1044) metal coordination : bond 0.00384 ( 4) metal coordination : angle 2.64333 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2404.09 seconds wall clock time: 42 minutes 0.01 seconds (2520.01 seconds total)