Starting phenix.real_space_refine on Wed Jan 14 01:11:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d7w_27236/01_2026/8d7w_27236.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d7w_27236/01_2026/8d7w_27236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d7w_27236/01_2026/8d7w_27236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d7w_27236/01_2026/8d7w_27236.map" model { file = "/net/cci-nas-00/data/ceres_data/8d7w_27236/01_2026/8d7w_27236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d7w_27236/01_2026/8d7w_27236.cif" } resolution = 3.1 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= 0.057 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 6924 2.51 5 N 1886 2.21 5 O 2075 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 15 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: 10943 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1127, 7918 Classifications: {'peptide': 1127} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 283} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 1086} Chain breaks: 2 Unresolved non-hydrogen bonds: 935 Unresolved non-hydrogen angles: 1188 Unresolved non-hydrogen dihedrals: 745 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'GLU:plan': 26, 'ASP:plan': 17, 'ARG:plan': 16, 'GLN:plan1': 17, 'HIS:plan': 8, 'TRP:plan': 3, 'ASN:plan1': 13, 'PHE:plan': 7, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 479 Chain: "B" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2982 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 21, 'TRANS': 362} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 7, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 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 10118 SG CYS B 323 41.662 84.570 27.551 1.00190.39 S ATOM 10134 SG CYS B 326 40.056 87.987 26.927 1.00203.74 S ATOM 10638 SG CYS B 391 39.203 85.177 24.495 1.00219.45 S ATOM 10657 SG CYS B 394 42.607 86.800 24.624 1.00236.11 S Time building chain proxies: 2.76, per 1000 atoms: 0.25 Number of scatterers: 10943 At special positions: 0 Unit cell: (89.7, 108.1, 157.55, 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 2075 8.00 N 1886 7.00 C 6924 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: 0.96 Conformation dependent library (CDL) restraints added in 576.5 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 391 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 323 " 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: 22 helices and 27 sheets defined 12.8% alpha, 37.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 381 through 384 Processing helix chain 'A' and resid 756 through 760 removed outlier: 4.080A pdb=" N ALA A 760 " --> pdb=" O SER A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 1044 through 1060 removed outlier: 3.753A pdb=" N LYS A1060 " --> pdb=" O ASN A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1068 removed outlier: 4.290A pdb=" N ILE A1068 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1075 Processing helix chain 'A' and resid 1091 through 1096 Processing helix chain 'A' and resid 1097 through 1100 removed outlier: 3.808A pdb=" N ILE A1100 " --> pdb=" O PHE A1097 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1097 through 1100' Processing helix chain 'A' and resid 1101 through 1109 Processing helix chain 'A' and resid 1126 through 1138 removed outlier: 3.672A pdb=" N GLU A1135 " --> pdb=" O LYS A1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.527A pdb=" N GLY B 151 " --> pdb=" O GLN B 148 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 152 " --> pdb=" O ASP B 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 152' Processing helix chain 'B' and resid 200 through 207 removed outlier: 4.073A pdb=" N LYS B 204 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N CYS B 205 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE B 207 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 232 Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.909A pdb=" N ASN B 236 " --> pdb=" O HIS B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 removed outlier: 3.717A pdb=" N TYR B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 265 Processing helix chain 'B' and resid 276 through 288 Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.521A pdb=" N ILE B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) 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: 3.673A pdb=" N VAL A1006 " --> pdb=" O GLY A1031 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLY A1026 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER A1042 " --> pdb=" O GLY A1026 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A1030 " --> pdb=" O GLY A1038 " (cutoff:3.500A) removed outlier: 6.443A 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: 5.880A pdb=" N VAL A 43 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 67 removed outlier: 3.689A pdb=" N THR A 81 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ALA A 86 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N HIS A 105 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.415A 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: 4.549A pdb=" N LEU A 135 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.718A 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: 6.694A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE A 169 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 7.333A 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: 6.912A 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: 6.747A pdb=" N LEU A 272 " --> pdb=" O HIS A 261 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ARG A 263 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ARG A 270 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP A 275 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.688A 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: 4.059A pdb=" N GLU A 289 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A 296 " --> pdb=" O GLU A 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.879A pdb=" N VAL A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER A 331 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR A 352 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 333 " --> pdb=" O MET A 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 362 through 365 removed outlier: 3.544A pdb=" N ARG A 388 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 396 through 403 removed outlier: 5.283A pdb=" N GLU A 398 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N THR A 703 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A 690 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 682 " --> pdb=" O SER A 690 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 410 through 413 removed outlier: 3.868A pdb=" N THR A 424 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A 425 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 459 through 463 removed outlier: 3.755A pdb=" N GLN A 467 " --> pdb=" O VAL A 463 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 498 through 503 removed outlier: 3.546A pdb=" N VAL A 500 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 516 " --> pdb=" O THR A 532 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLN A 520 " --> pdb=" O GLN A 528 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLN A 528 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N HIS A 522 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU A 526 " --> pdb=" O HIS A 522 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.920A pdb=" N CYS A 540 " --> pdb=" O GLY A 559 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 588 through 594 removed outlier: 3.962A pdb=" N CYS A 604 " --> pdb=" O PHE A 612 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 637 through 639 removed outlier: 3.735A pdb=" N THR A 657 " --> pdb=" O ALA A 651 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.807A pdb=" N SER A 738 " --> pdb=" O PRO A 721 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS A 723 " --> pdb=" O LEU A 736 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.807A pdb=" N SER A 738 " --> pdb=" O PRO A 721 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS A 723 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASP A 795 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 801 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER A 762 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N GLN A 806 " --> pdb=" O SER A 762 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N SER A 764 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 811 through 819 removed outlier: 5.334A pdb=" N ALA A 813 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA A 834 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLN A 845 " --> pdb=" O MET A 835 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 866 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN A 852 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N THR A 860 " --> pdb=" O GLN A 852 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N SER A 854 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 870 through 876 removed outlier: 4.195A pdb=" N SER A 872 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 888 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN A 904 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU A 890 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 913 through 917 removed outlier: 4.178A pdb=" N ALA A 946 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA A 934 " --> pdb=" O GLU A 944 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A 944 " --> pdb=" O ALA A 934 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 956 through 959 removed outlier: 3.906A pdb=" N ALA A 956 " --> pdb=" O ALA A 968 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 974 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU A 997 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL A 976 " --> pdb=" O VAL A 995 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 65 through 66 removed outlier: 7.005A pdb=" N GLY B 136 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ARG B 164 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR B 138 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS B 158 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR B 144 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS B 156 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 78 through 82 removed outlier: 7.241A pdb=" N GLN B 179 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU B 170 " --> pdb=" O GLN B 179 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LYS B 181 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS B 156 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR B 144 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS B 158 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR B 138 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ARG B 164 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLY B 136 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE B 135 " --> pdb=" O ALA B 124 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AC9, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.728A pdb=" N GLY B 399 " --> pdb=" O ALA B 389 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1122 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: 2.60 Time building geometry restraints manager: 1.29 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: 1885 1.28 - 1.41: 2672 1.41 - 1.54: 6498 1.54 - 1.68: 19 1.68 - 1.81: 82 Bond restraints: 11156 Sorted by residual: bond pdb=" N QFC B 502 " pdb=" C5 QFC B 502 " ideal model delta sigma weight residual 1.372 1.410 -0.038 2.00e-02 2.50e+03 3.66e+00 bond pdb=" N ASP A 318 " pdb=" CA ASP A 318 " ideal model delta sigma weight residual 1.454 1.477 -0.023 1.34e-02 5.57e+03 2.95e+00 bond pdb=" C LEU B 97 " pdb=" O LEU B 97 " ideal model delta sigma weight residual 1.249 1.236 0.012 8.50e-03 1.38e+04 2.13e+00 bond pdb=" CA VAL A 870 " pdb=" CB VAL A 870 " ideal model delta sigma weight residual 1.540 1.523 0.017 1.36e-02 5.41e+03 1.57e+00 bond pdb=" CG GLU B 147 " pdb=" CD GLU B 147 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.55e+00 ... (remaining 11151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 14910 1.87 - 3.74: 275 3.74 - 5.61: 28 5.61 - 7.48: 6 7.48 - 9.35: 1 Bond angle restraints: 15220 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 103.15 110.46 -7.31 9.70e-01 1.06e+00 5.68e+01 angle pdb=" C SER A1021 " pdb=" CA SER A1021 " pdb=" CB SER A1021 " ideal model delta sigma weight residual 115.89 110.26 5.63 1.32e+00 5.74e-01 1.82e+01 angle pdb=" CB LYS B 407 " pdb=" CG LYS B 407 " pdb=" CD LYS B 407 " ideal model delta sigma weight residual 111.30 118.14 -6.84 2.30e+00 1.89e-01 8.84e+00 angle pdb=" N ASP A 184 " pdb=" CA ASP A 184 " pdb=" C ASP A 184 " ideal model delta sigma weight residual 108.55 104.25 4.30 1.56e+00 4.11e-01 7.59e+00 angle pdb=" CA LEU B 202 " pdb=" CB LEU B 202 " pdb=" CG LEU B 202 " ideal model delta sigma weight residual 116.30 125.65 -9.35 3.50e+00 8.16e-02 7.14e+00 ... (remaining 15215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6060 17.96 - 35.92: 505 35.92 - 53.88: 77 53.88 - 71.84: 13 71.84 - 89.80: 12 Dihedral angle restraints: 6667 sinusoidal: 2284 harmonic: 4383 Sorted by residual: dihedral pdb=" CA GLU B 146 " pdb=" C GLU B 146 " pdb=" N GLU B 147 " pdb=" CA GLU B 147 " ideal model delta harmonic sigma weight residual -180.00 -161.94 -18.06 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ILE A 707 " pdb=" C ILE A 707 " pdb=" N GLN A 708 " pdb=" CA GLN A 708 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CB GLU A1069 " pdb=" CG GLU A1069 " pdb=" CD GLU A1069 " pdb=" OE1 GLU A1069 " ideal model delta sinusoidal sigma weight residual 0.00 89.80 -89.80 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 6664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1236 0.042 - 0.084: 372 0.084 - 0.126: 151 0.126 - 0.168: 9 0.168 - 0.210: 4 Chirality restraints: 1772 Sorted by residual: chirality pdb=" CA ASP A 184 " pdb=" N ASP A 184 " pdb=" C ASP A 184 " pdb=" CB ASP A 184 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB VAL A 995 " pdb=" CA VAL A 995 " pdb=" CG1 VAL A 995 " pdb=" CG2 VAL A 995 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.12e-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 8.84e-01 ... (remaining 1769 not shown) Planarity restraints: 1997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" O QFC B 502 " 0.032 2.00e-02 2.50e+03 1.77e-02 9.35e+00 pdb=" C14 QFC B 502 " 0.006 2.00e-02 2.50e+03 pdb=" C15 QFC B 502 " -0.005 2.00e-02 2.50e+03 pdb=" C16 QFC B 502 " -0.016 2.00e-02 2.50e+03 pdb=" C17 QFC B 502 " -0.011 2.00e-02 2.50e+03 pdb=" C18 QFC B 502 " -0.002 2.00e-02 2.50e+03 pdb=" C19 QFC B 502 " 0.013 2.00e-02 2.50e+03 pdb=" C20 QFC B 502 " -0.033 2.00e-02 2.50e+03 pdb=" C21 QFC B 502 " 0.001 2.00e-02 2.50e+03 pdb=" C22 QFC B 502 " -0.011 2.00e-02 2.50e+03 pdb=" N2 QFC B 502 " -0.003 2.00e-02 2.50e+03 pdb=" O1 QFC B 502 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N QFC B 502 " 0.023 2.00e-02 2.50e+03 1.11e-02 3.07e+00 pdb=" C QFC B 502 " -0.004 2.00e-02 2.50e+03 pdb=" C1 QFC B 502 " -0.009 2.00e-02 2.50e+03 pdb=" C2 QFC B 502 " -0.009 2.00e-02 2.50e+03 pdb=" C3 QFC B 502 " -0.012 2.00e-02 2.50e+03 pdb=" C31 QFC B 502 " 0.004 2.00e-02 2.50e+03 pdb=" C4 QFC B 502 " -0.007 2.00e-02 2.50e+03 pdb=" C5 QFC B 502 " 0.000 2.00e-02 2.50e+03 pdb=" F QFC B 502 " -0.003 2.00e-02 2.50e+03 pdb=" N4 QFC B 502 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 125 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO A 126 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " 0.024 5.00e-02 4.00e+02 ... (remaining 1994 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 775 2.74 - 3.28: 10401 3.28 - 3.82: 17173 3.82 - 4.36: 20003 4.36 - 4.90: 36243 Nonbonded interactions: 84595 Sorted by model distance: nonbonded pdb=" OE2 GLU A 811 " pdb=" OG1 THR A 833 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASP A 299 " pdb=" N LEU A 300 " model vdw 2.203 3.120 nonbonded pdb=" NE2 GLN A 727 " pdb=" OG1 THR A 827 " model vdw 2.220 3.120 nonbonded pdb=" OE1 GLU A 40 " pdb=" OH TYR A 42 " model vdw 2.248 3.040 nonbonded pdb=" O SER A1071 " pdb=" OG SER A1075 " model vdw 2.262 3.040 ... (remaining 84590 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.830 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: 16.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 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 0.039 11160 Z= 0.162 Angle : 0.621 9.354 15226 Z= 0.332 Chirality : 0.046 0.210 1772 Planarity : 0.004 0.043 1997 Dihedral : 13.972 89.800 3835 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.72 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: -1.58 (0.22), residues: 1503 helix: 0.01 (0.40), residues: 174 sheet: -0.38 (0.23), residues: 586 loop : -1.88 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 301 TYR 0.013 0.002 TYR A 42 PHE 0.019 0.002 PHE B 338 TRP 0.015 0.002 TRP A 207 HIS 0.003 0.001 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00366 (11156) covalent geometry : angle 0.61616 (15220) hydrogen bonds : bond 0.17575 ( 411) hydrogen bonds : angle 7.94441 ( 1122) metal coordination : bond 0.00782 ( 4) metal coordination : angle 3.85291 ( 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 187 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 226 PHE cc_start: 0.7484 (m-80) cc_final: 0.7004 (m-80) REVERT: A 343 GLN cc_start: 0.6794 (pt0) cc_final: 0.6434 (tm-30) REVERT: B 154 ILE cc_start: 0.7338 (mt) cc_final: 0.7056 (mp) REVERT: B 276 ASN cc_start: 0.7317 (t0) cc_final: 0.6627 (t0) REVERT: B 335 ASN cc_start: 0.7330 (m-40) cc_final: 0.7063 (m-40) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.0944 time to fit residues: 26.3909 Evaluate side-chains 137 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 978 GLN B 73 HIS B 79 GLN B 203 ASN B 390 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.160600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.116910 restraints weight = 16031.565| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.90 r_work: 0.3394 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 11160 Z= 0.279 Angle : 0.673 6.757 15226 Z= 0.351 Chirality : 0.049 0.182 1772 Planarity : 0.005 0.045 1997 Dihedral : 5.955 64.517 1639 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.32 % Favored : 92.42 % Rotamer: Outliers : 2.05 % Allowed : 9.69 % Favored : 88.26 % 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: -0.17 (0.39), residues: 175 sheet: -0.59 (0.22), residues: 569 loop : -1.93 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1080 TYR 0.018 0.002 TYR A 42 PHE 0.020 0.002 PHE A 829 TRP 0.016 0.002 TRP A 207 HIS 0.007 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00667 (11156) covalent geometry : angle 0.66828 (15220) hydrogen bonds : bond 0.04393 ( 411) hydrogen bonds : angle 6.46690 ( 1122) metal coordination : bond 0.00969 ( 4) metal coordination : angle 4.09258 ( 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 166 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.357 Fit side-chains REVERT: A 111 ARG cc_start: 0.7930 (tpt170) cc_final: 0.7462 (ttt90) REVERT: A 166 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7248 (m-30) REVERT: A 343 GLN cc_start: 0.6857 (pt0) cc_final: 0.6373 (tm-30) REVERT: A 368 GLU cc_start: 0.6101 (mt-10) cc_final: 0.5874 (mt-10) REVERT: A 1080 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.7031 (ptp-170) outliers start: 21 outliers final: 12 residues processed: 153 average time/residue: 0.0920 time to fit residues: 20.9683 Evaluate side-chains 146 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 1080 ARG Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 355 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 133 optimal weight: 0.9980 chunk 100 optimal weight: 0.0000 chunk 49 optimal weight: 40.0000 chunk 14 optimal weight: 0.0570 chunk 96 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 overall best weight: 0.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN B 73 HIS ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.164505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.120823 restraints weight = 16076.743| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.22 r_work: 0.3444 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11160 Z= 0.105 Angle : 0.531 6.545 15226 Z= 0.277 Chirality : 0.044 0.158 1772 Planarity : 0.004 0.044 1997 Dihedral : 5.120 49.268 1639 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.52 % Favored : 93.21 % Rotamer: Outliers : 1.66 % Allowed : 13.50 % Favored : 84.83 % 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: -1.69 (0.21), residues: 1503 helix: 0.04 (0.40), residues: 176 sheet: -0.61 (0.22), residues: 585 loop : -1.83 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 373 TYR 0.015 0.001 TYR A 42 PHE 0.012 0.001 PHE A 851 TRP 0.017 0.001 TRP A 207 HIS 0.002 0.000 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00240 (11156) covalent geometry : angle 0.52596 (15220) hydrogen bonds : bond 0.03403 ( 411) hydrogen bonds : angle 5.84000 ( 1122) metal coordination : bond 0.00771 ( 4) metal coordination : angle 3.58634 ( 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 174 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.430 Fit side-chains REVERT: A 111 ARG cc_start: 0.7996 (tpt170) cc_final: 0.7506 (ttt90) REVERT: A 166 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7206 (m-30) REVERT: A 226 PHE cc_start: 0.7628 (m-80) cc_final: 0.7033 (m-80) REVERT: A 1080 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.7089 (ptm160) outliers start: 17 outliers final: 10 residues processed: 161 average time/residue: 0.0936 time to fit residues: 22.2260 Evaluate side-chains 146 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1080 ARG Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 192 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 110 optimal weight: 0.7980 chunk 100 optimal weight: 0.0010 chunk 107 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 50.0000 chunk 111 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 117 optimal weight: 0.1980 chunk 11 optimal weight: 7.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 HIS B 203 ASN B 276 ASN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.163762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.119651 restraints weight = 15982.626| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.96 r_work: 0.3441 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11160 Z= 0.125 Angle : 0.525 6.058 15226 Z= 0.274 Chirality : 0.045 0.158 1772 Planarity : 0.004 0.042 1997 Dihedral : 4.829 40.524 1639 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.39 % Favored : 93.35 % Rotamer: Outliers : 1.96 % Allowed : 14.87 % Favored : 83.17 % 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: -1.68 (0.21), residues: 1503 helix: 0.16 (0.40), residues: 175 sheet: -0.63 (0.21), residues: 590 loop : -1.83 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 301 TYR 0.013 0.001 TYR A 42 PHE 0.012 0.001 PHE A 851 TRP 0.014 0.001 TRP A 207 HIS 0.007 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00296 (11156) covalent geometry : angle 0.52046 (15220) hydrogen bonds : bond 0.03255 ( 411) hydrogen bonds : angle 5.58992 ( 1122) metal coordination : bond 0.00724 ( 4) metal coordination : angle 3.42313 ( 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 164 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.498 Fit side-chains REVERT: A 111 ARG cc_start: 0.7977 (tpt170) cc_final: 0.7569 (ttt90) REVERT: A 130 MET cc_start: 0.8249 (ptm) cc_final: 0.8041 (ptm) REVERT: A 166 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7308 (m-30) REVERT: A 226 PHE cc_start: 0.7634 (m-80) cc_final: 0.7006 (m-80) REVERT: B 50 ASP cc_start: 0.8059 (t0) cc_final: 0.7830 (t70) outliers start: 20 outliers final: 15 residues processed: 151 average time/residue: 0.0964 time to fit residues: 21.2780 Evaluate side-chains 150 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 613 TYR Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 335 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 61 optimal weight: 30.0000 chunk 140 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS B 73 HIS ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.159919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.115529 restraints weight = 15962.166| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.92 r_work: 0.3413 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11160 Z= 0.266 Angle : 0.616 5.210 15226 Z= 0.321 Chirality : 0.047 0.163 1772 Planarity : 0.004 0.042 1997 Dihedral : 5.160 37.640 1639 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.12 % Favored : 91.62 % Rotamer: Outliers : 2.54 % Allowed : 15.56 % Favored : 81.90 % 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: -1.81 (0.21), residues: 1503 helix: -0.08 (0.39), residues: 177 sheet: -0.67 (0.22), residues: 572 loop : -1.90 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 164 TYR 0.015 0.002 TYR B 125 PHE 0.021 0.002 PHE A1030 TRP 0.012 0.002 TRP A 207 HIS 0.009 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00632 (11156) covalent geometry : angle 0.61320 (15220) hydrogen bonds : bond 0.03898 ( 411) hydrogen bonds : angle 5.83368 ( 1122) metal coordination : bond 0.00676 ( 4) metal coordination : angle 2.90558 ( 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 155 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.397 Fit side-chains REVERT: A 165 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8537 (mt) REVERT: A 166 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7174 (m-30) REVERT: A 343 GLN cc_start: 0.6870 (pt0) cc_final: 0.6346 (tm-30) REVERT: A 812 TYR cc_start: 0.7977 (t80) cc_final: 0.7665 (t80) REVERT: B 50 ASP cc_start: 0.8235 (t0) cc_final: 0.7915 (t0) outliers start: 26 outliers final: 14 residues processed: 144 average time/residue: 0.0973 time to fit residues: 20.5674 Evaluate side-chains 137 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 613 TYR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 335 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 90 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 140 optimal weight: 20.0000 chunk 119 optimal weight: 0.5980 chunk 64 optimal weight: 8.9990 chunk 41 optimal weight: 0.0020 chunk 23 optimal weight: 0.7980 chunk 52 optimal weight: 20.0000 chunk 144 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS B 203 ASN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.163275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.119412 restraints weight = 15912.831| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.95 r_work: 0.3467 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11160 Z= 0.109 Angle : 0.514 6.588 15226 Z= 0.268 Chirality : 0.044 0.158 1772 Planarity : 0.004 0.041 1997 Dihedral : 4.560 29.107 1639 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.45 % Favored : 93.35 % Rotamer: Outliers : 1.47 % Allowed : 17.12 % Favored : 81.41 % 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: -1.65 (0.21), residues: 1503 helix: 0.14 (0.40), residues: 177 sheet: -0.60 (0.22), residues: 585 loop : -1.81 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 198 TYR 0.014 0.001 TYR A 42 PHE 0.013 0.001 PHE B 150 TRP 0.017 0.001 TRP A 207 HIS 0.001 0.000 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00254 (11156) covalent geometry : angle 0.50946 (15220) hydrogen bonds : bond 0.03065 ( 411) hydrogen bonds : angle 5.37754 ( 1122) metal coordination : bond 0.00685 ( 4) metal coordination : angle 3.29871 ( 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 154 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.331 Fit side-chains REVERT: A 166 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.7124 (m-30) REVERT: A 299 ASP cc_start: 0.7161 (t0) cc_final: 0.6777 (t0) REVERT: A 1107 GLU cc_start: 0.8680 (tp30) cc_final: 0.8403 (tp30) REVERT: B 50 ASP cc_start: 0.8496 (t0) cc_final: 0.8208 (t0) REVERT: B 60 LEU cc_start: 0.8202 (tp) cc_final: 0.7903 (mp) outliers start: 15 outliers final: 10 residues processed: 147 average time/residue: 0.0898 time to fit residues: 19.7957 Evaluate side-chains 143 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 33 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 48 optimal weight: 30.0000 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 240 HIS B 73 HIS ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.161535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.117245 restraints weight = 15890.971| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.93 r_work: 0.3409 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11160 Z= 0.172 Angle : 0.551 6.328 15226 Z= 0.287 Chirality : 0.045 0.159 1772 Planarity : 0.004 0.041 1997 Dihedral : 4.656 29.353 1639 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.58 % Favored : 92.22 % Rotamer: Outliers : 1.76 % Allowed : 17.32 % Favored : 80.92 % 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: -1.62 (0.21), residues: 1503 helix: 0.21 (0.40), residues: 175 sheet: -0.57 (0.22), residues: 578 loop : -1.80 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 198 TYR 0.012 0.001 TYR A 42 PHE 0.017 0.002 PHE A1030 TRP 0.012 0.001 TRP A 207 HIS 0.003 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00410 (11156) covalent geometry : angle 0.54840 (15220) hydrogen bonds : bond 0.03313 ( 411) hydrogen bonds : angle 5.43035 ( 1122) metal coordination : bond 0.00681 ( 4) metal coordination : angle 2.94812 ( 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 154 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.424 Fit side-chains REVERT: A 166 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.7120 (m-30) REVERT: A 1107 GLU cc_start: 0.8693 (tp30) cc_final: 0.8384 (tp30) REVERT: B 50 ASP cc_start: 0.8564 (t0) cc_final: 0.8246 (t0) outliers start: 18 outliers final: 13 residues processed: 147 average time/residue: 0.0928 time to fit residues: 20.2386 Evaluate side-chains 148 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 335 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 95 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 40 optimal weight: 40.0000 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 76 optimal weight: 0.3980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 HIS B 203 ASN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.159943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.116187 restraints weight = 15982.450| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.89 r_work: 0.3417 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11160 Z= 0.230 Angle : 0.596 7.589 15226 Z= 0.310 Chirality : 0.047 0.160 1772 Planarity : 0.004 0.042 1997 Dihedral : 4.871 30.730 1639 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.72 % Favored : 92.08 % Rotamer: Outliers : 2.05 % Allowed : 17.12 % Favored : 80.82 % 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: -1.72 (0.21), residues: 1503 helix: 0.11 (0.40), residues: 175 sheet: -0.61 (0.22), residues: 570 loop : -1.88 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 198 TYR 0.012 0.002 TYR B 363 PHE 0.020 0.002 PHE A1030 TRP 0.012 0.002 TRP A 207 HIS 0.014 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00548 (11156) covalent geometry : angle 0.59344 (15220) hydrogen bonds : bond 0.03579 ( 411) hydrogen bonds : angle 5.55816 ( 1122) metal coordination : bond 0.00676 ( 4) metal coordination : angle 2.91852 ( 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 148 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.335 Fit side-chains REVERT: A 166 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7437 (m-30) REVERT: A 299 ASP cc_start: 0.7509 (t0) cc_final: 0.7133 (t0) REVERT: B 50 ASP cc_start: 0.8603 (t0) cc_final: 0.8256 (t70) REVERT: B 73 HIS cc_start: 0.7504 (OUTLIER) cc_final: 0.6965 (t70) REVERT: B 268 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.7000 (pp) outliers start: 21 outliers final: 14 residues processed: 139 average time/residue: 0.0891 time to fit residues: 18.3974 Evaluate side-chains 143 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 298 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.2980 chunk 112 optimal weight: 5.9990 chunk 113 optimal weight: 0.0870 chunk 105 optimal weight: 0.4980 chunk 133 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 44 optimal weight: 50.0000 chunk 23 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 HIS B 203 ASN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.162061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.118041 restraints weight = 15788.726| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.93 r_work: 0.3450 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11160 Z= 0.126 Angle : 0.537 7.187 15226 Z= 0.280 Chirality : 0.044 0.154 1772 Planarity : 0.004 0.042 1997 Dihedral : 4.620 29.576 1639 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.32 % Favored : 92.48 % Rotamer: Outliers : 1.37 % Allowed : 18.10 % 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: -1.64 (0.21), residues: 1503 helix: 0.14 (0.40), residues: 176 sheet: -0.54 (0.22), residues: 570 loop : -1.83 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 198 TYR 0.014 0.001 TYR A 42 PHE 0.015 0.001 PHE B 150 TRP 0.015 0.001 TRP A 207 HIS 0.013 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00292 (11156) covalent geometry : angle 0.53310 (15220) hydrogen bonds : bond 0.03113 ( 411) hydrogen bonds : angle 5.35286 ( 1122) metal coordination : bond 0.00675 ( 4) metal coordination : angle 3.13679 ( 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 149 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.413 Fit side-chains REVERT: A 166 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7154 (m-30) REVERT: A 299 ASP cc_start: 0.7171 (t0) cc_final: 0.6827 (t0) REVERT: A 1107 GLU cc_start: 0.8695 (tp30) cc_final: 0.8368 (tp30) REVERT: B 50 ASP cc_start: 0.8507 (t0) cc_final: 0.8192 (t70) REVERT: B 73 HIS cc_start: 0.7362 (OUTLIER) cc_final: 0.6983 (t70) REVERT: B 268 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7033 (pp) outliers start: 14 outliers final: 11 residues processed: 143 average time/residue: 0.0932 time to fit residues: 19.6134 Evaluate side-chains 141 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 298 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 49 optimal weight: 40.0000 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 0.0060 chunk 107 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 121 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 HIS B 73 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.159308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.114959 restraints weight = 16014.988| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.32 r_work: 0.3367 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 11160 Z= 0.306 Angle : 0.662 7.578 15226 Z= 0.345 Chirality : 0.048 0.164 1772 Planarity : 0.005 0.041 1997 Dihedral : 5.096 32.526 1639 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.98 % Favored : 91.82 % Rotamer: Outliers : 1.57 % Allowed : 18.10 % Favored : 80.33 % 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: -1.92 (0.21), residues: 1503 helix: -0.14 (0.39), residues: 176 sheet: -0.75 (0.22), residues: 557 loop : -1.97 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 373 TYR 0.014 0.002 TYR A 660 PHE 0.024 0.002 PHE A1030 TRP 0.012 0.002 TRP B 415 HIS 0.016 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00732 (11156) covalent geometry : angle 0.65951 (15220) hydrogen bonds : bond 0.03935 ( 411) hydrogen bonds : angle 5.72482 ( 1122) metal coordination : bond 0.00887 ( 4) metal coordination : angle 3.12585 ( 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 142 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.430 Fit side-chains REVERT: A 165 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8546 (mt) REVERT: A 166 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7231 (m-30) REVERT: B 50 ASP cc_start: 0.8397 (t0) cc_final: 0.8012 (t0) REVERT: B 73 HIS cc_start: 0.7523 (OUTLIER) cc_final: 0.7116 (t70) REVERT: B 268 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7160 (pp) outliers start: 16 outliers final: 10 residues processed: 137 average time/residue: 0.0918 time to fit residues: 18.7559 Evaluate side-chains 139 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 298 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 116 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 129 optimal weight: 0.0770 chunk 110 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 42 optimal weight: 50.0000 chunk 21 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 797 HIS B 73 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.162119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.118033 restraints weight = 15924.636| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.93 r_work: 0.3455 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11160 Z= 0.140 Angle : 0.559 7.408 15226 Z= 0.291 Chirality : 0.045 0.153 1772 Planarity : 0.004 0.041 1997 Dihedral : 4.743 29.628 1639 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.05 % Favored : 92.75 % Rotamer: Outliers : 1.17 % Allowed : 18.88 % Favored : 79.94 % 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: -0.00 (0.40), residues: 176 sheet: -0.70 (0.22), residues: 560 loop : -1.87 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 373 TYR 0.013 0.001 TYR A 42 PHE 0.015 0.001 PHE B 150 TRP 0.015 0.002 TRP A 207 HIS 0.006 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00331 (11156) covalent geometry : angle 0.55549 (15220) hydrogen bonds : bond 0.03193 ( 411) hydrogen bonds : angle 5.43357 ( 1122) metal coordination : bond 0.00807 ( 4) metal coordination : angle 3.39251 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2719.70 seconds wall clock time: 47 minutes 18.55 seconds (2838.55 seconds total)