Starting phenix.real_space_refine on Fri Jul 3 05:25:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7whw_32513/07_2026/7whw_32513.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whw_32513/07_2026/7whw_32513.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/7whw_32513/07_2026/7whw_32513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whw_32513/07_2026/7whw_32513.map" model { file = "/net/cci-nas-00/data/ceres_data/7whw_32513/07_2026/7whw_32513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whw_32513/07_2026/7whw_32513.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7whw_32513/07_2026/7whw_32513.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7whw_32513/07_2026/7whw_32513.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= 0.003 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 P 3 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 7706 2.51 5 N 1987 2.21 5 O 2224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11978 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1126, 8973 Classifications: {'peptide': 1126} Link IDs: {'PTRANS': 35, 'TRANS': 1090} Chain breaks: 2 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2934 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.92, per 1000 atoms: 0.24 Number of scatterers: 11978 At special positions: 0 Unit cell: (136.96, 109.14, 129.47, 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) S 57 16.00 P 3 15.00 Mg 1 11.99 O 2224 8.00 N 1987 7.00 C 7706 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.02 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.02 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN B 240 " Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 549.7 milliseconds 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2782 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 13 sheets defined 41.3% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 205 through 215 removed outlier: 4.140A pdb=" N LYS A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 232 removed outlier: 3.938A pdb=" N PHE A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 244 through 275 removed outlier: 4.291A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 465 removed outlier: 3.505A pdb=" N ARG A 464 " --> pdb=" O ASP A 461 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR A 465 " --> pdb=" O ILE A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 461 through 465' Processing helix chain 'A' and resid 544 through 576 removed outlier: 4.836A pdb=" N ASN A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE A 551 " --> pdb=" O ARG A 547 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 552 " --> pdb=" O GLU A 548 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 554 " --> pdb=" O ASN A 550 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A 574 " --> pdb=" O ALA A 570 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 609 removed outlier: 3.702A pdb=" N TRP A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 634 Processing helix chain 'A' and resid 654 through 660 Processing helix chain 'A' and resid 695 through 703 removed outlier: 4.050A pdb=" N GLY A 699 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 700 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ARG A 701 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS A 702 " --> pdb=" O GLY A 699 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG A 703 " --> pdb=" O LEU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 719 removed outlier: 3.631A pdb=" N GLU A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 777 removed outlier: 4.214A pdb=" N ARG A 765 " --> pdb=" O GLU A 761 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 768 " --> pdb=" O GLN A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 812 removed outlier: 3.569A pdb=" N ALA A 803 " --> pdb=" O PRO A 799 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 804 " --> pdb=" O ASP A 800 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 805 " --> pdb=" O GLU A 801 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 880 Processing helix chain 'A' and resid 892 through 903 removed outlier: 3.969A pdb=" N LEU A 898 " --> pdb=" O GLU A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 933 removed outlier: 5.439A pdb=" N LYS A 925 " --> pdb=" O SER A 921 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TRP A 926 " --> pdb=" O GLU A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 935 No H-bonds generated for 'chain 'A' and resid 934 through 935' Processing helix chain 'A' and resid 936 through 941 removed outlier: 3.950A pdb=" N ASN A 939 " --> pdb=" O SER A 936 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG A 940 " --> pdb=" O LEU A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 948 removed outlier: 4.187A pdb=" N VAL A 946 " --> pdb=" O ASP A 942 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 947 " --> pdb=" O GLU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 975 removed outlier: 3.838A pdb=" N CYS A 974 " --> pdb=" O GLY A 970 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE A 975 " --> pdb=" O VAL A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 970 through 975' Processing helix chain 'A' and resid 992 through 1001 Processing helix chain 'A' and resid 1034 through 1044 removed outlier: 3.683A pdb=" N SER A1038 " --> pdb=" O ASP A1034 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A1039 " --> pdb=" O ALA A1035 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A1042 " --> pdb=" O SER A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1060 Processing helix chain 'A' and resid 1073 through 1081 Processing helix chain 'A' and resid 1086 through 1094 removed outlier: 3.674A pdb=" N LEU A1093 " --> pdb=" O LYS A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1121 Processing helix chain 'A' and resid 1131 through 1135 removed outlier: 3.831A pdb=" N VAL A1135 " --> pdb=" O SER A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1141 Processing helix chain 'A' and resid 1153 through 1158 removed outlier: 3.614A pdb=" N MET A1157 " --> pdb=" O ARG A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1168 through 1175 Processing helix chain 'A' and resid 1175 through 1200 Proline residue: A1189 - end of helix removed outlier: 3.514A pdb=" N ASN A1195 " --> pdb=" O PHE A1191 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A1198 " --> pdb=" O LYS A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1208 removed outlier: 3.614A pdb=" N ILE A1207 " --> pdb=" O TRP A1204 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1240 removed outlier: 4.433A pdb=" N VAL A1234 " --> pdb=" O THR A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1252 Processing helix chain 'A' and resid 1253 through 1255 No H-bonds generated for 'chain 'A' and resid 1253 through 1255' Processing helix chain 'A' and resid 1256 through 1261 removed outlier: 3.570A pdb=" N ILE A1260 " --> pdb=" O TYR A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1293 Proline residue: A1288 - end of helix Processing helix chain 'A' and resid 1307 through 1329 Processing helix chain 'A' and resid 1335 through 1347 Processing helix chain 'A' and resid 1347 through 1357 removed outlier: 4.016A pdb=" N THR A1353 " --> pdb=" O VAL A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1373 removed outlier: 3.552A pdb=" N ARG A1371 " --> pdb=" O LYS A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1375 through 1383 removed outlier: 3.844A pdb=" N TRP A1379 " --> pdb=" O ALA A1375 " (cutoff:3.500A) Processing helix chain 'A' and resid 1386 through 1404 Proline residue: A1392 - end of helix Processing helix chain 'A' and resid 1406 through 1417 removed outlier: 3.625A pdb=" N HIS A1417 " --> pdb=" O GLU A1413 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 98 removed outlier: 3.535A pdb=" N LEU B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) Proline residue: B 77 - end of helix removed outlier: 3.561A pdb=" N ILE B 88 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 114 removed outlier: 3.599A pdb=" N ALA B 114 " --> pdb=" O CYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.763A pdb=" N LEU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 266 through 272 removed outlier: 3.529A pdb=" N ARG B 272 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 372 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 409 removed outlier: 3.562A pdb=" N GLY A 520 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 445 through 448 Processing sheet with id=AA3, first strand: chain 'A' and resid 485 through 488 removed outlier: 4.417A pdb=" N MET A 485 " --> pdb=" O GLU A 498 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A 498 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TRP A 487 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG A 496 " --> pdb=" O TRP A 487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 663 through 664 removed outlier: 6.189A pdb=" N ILE A 664 " --> pdb=" O TRP A 986 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU A 985 " --> pdb=" O VAL A1100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 682 through 684 Processing sheet with id=AA6, first strand: chain 'A' and resid 781 through 783 removed outlier: 3.504A pdb=" N ASP A 793 " --> pdb=" O GLU A 783 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 813 through 817 removed outlier: 6.920A pdb=" N ILE A 824 " --> pdb=" O VAL A 816 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 848 through 851 removed outlier: 5.865A pdb=" N GLN A 915 " --> pdb=" O LEU A 957 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LEU A 957 " --> pdb=" O GLN A 915 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1012 through 1013 Processing sheet with id=AB1, first strand: chain 'A' and resid 1145 through 1147 removed outlier: 6.306A pdb=" N GLY A1146 " --> pdb=" O ILE A1163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 126 through 129 removed outlier: 6.032A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU B 179 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N THR B 324 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 119 through 120 removed outlier: 5.628A pdb=" N ASP B 343 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N GLN B 246 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 227 through 228 removed outlier: 6.341A pdb=" N ILE B 227 " --> pdb=" O ALA B 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 409 hydrogen bonds defined for protein. 1125 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: 2.18 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2962 1.33 - 1.45: 2814 1.45 - 1.58: 6390 1.58 - 1.70: 6 1.70 - 1.82: 86 Bond restraints: 12258 Sorted by residual: bond pdb=" O2B ACP A1601 " pdb=" PB ACP A1601 " ideal model delta sigma weight residual 1.507 1.605 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" O3A ACP A1601 " pdb=" PB ACP A1601 " ideal model delta sigma weight residual 1.698 1.603 0.095 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C4 ACP A1601 " pdb=" C5 ACP A1601 " ideal model delta sigma weight residual 1.386 1.465 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" O3G ACP A1601 " pdb=" PG ACP A1601 " ideal model delta sigma weight residual 1.532 1.608 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C5 ACP A1601 " pdb=" C6 ACP A1601 " ideal model delta sigma weight residual 1.407 1.479 -0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 12253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 16156 3.00 - 6.00: 403 6.00 - 9.00: 61 9.00 - 12.00: 11 12.00 - 15.00: 3 Bond angle restraints: 16634 Sorted by residual: angle pdb=" N ILE A1086 " pdb=" CA ILE A1086 " pdb=" C ILE A1086 " ideal model delta sigma weight residual 113.53 107.28 6.25 9.80e-01 1.04e+00 4.07e+01 angle pdb=" CA ARG A1333 " pdb=" CB ARG A1333 " pdb=" CG ARG A1333 " ideal model delta sigma weight residual 114.10 124.64 -10.54 2.00e+00 2.50e-01 2.78e+01 angle pdb=" C LEU A1101 " pdb=" N CYS A1102 " pdb=" CA CYS A1102 " ideal model delta sigma weight residual 122.21 114.02 8.19 1.62e+00 3.81e-01 2.56e+01 angle pdb=" N LEU A1101 " pdb=" CA LEU A1101 " pdb=" C LEU A1101 " ideal model delta sigma weight residual 112.13 119.02 -6.89 1.37e+00 5.33e-01 2.53e+01 angle pdb=" C ASN B 240 " pdb=" CA ASN B 240 " pdb=" CB ASN B 240 " ideal model delta sigma weight residual 110.90 103.68 7.22 1.58e+00 4.01e-01 2.09e+01 ... (remaining 16629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.61: 7066 28.61 - 57.21: 154 57.21 - 85.82: 4 85.82 - 114.43: 1 114.43 - 143.03: 1 Dihedral angle restraints: 7226 sinusoidal: 2888 harmonic: 4338 Sorted by residual: dihedral pdb=" CA TYR A1219 " pdb=" C TYR A1219 " pdb=" N THR A1220 " pdb=" CA THR A1220 " ideal model delta harmonic sigma weight residual 180.00 134.93 45.07 0 5.00e+00 4.00e-02 8.12e+01 dihedral pdb=" CA VAL A1100 " pdb=" C VAL A1100 " pdb=" N LEU A1101 " pdb=" CA LEU A1101 " ideal model delta harmonic sigma weight residual -180.00 -141.67 -38.33 0 5.00e+00 4.00e-02 5.88e+01 dihedral pdb=" CA LEU A1101 " pdb=" C LEU A1101 " pdb=" N CYS A1102 " pdb=" CA CYS A1102 " ideal model delta harmonic sigma weight residual -180.00 -143.79 -36.21 0 5.00e+00 4.00e-02 5.24e+01 ... (remaining 7223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1393 0.070 - 0.139: 389 0.139 - 0.209: 50 0.209 - 0.278: 17 0.278 - 0.348: 3 Chirality restraints: 1852 Sorted by residual: chirality pdb=" CB ILE A 836 " pdb=" CA ILE A 836 " pdb=" CG1 ILE A 836 " pdb=" CG2 ILE A 836 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA ARG A1333 " pdb=" N ARG A1333 " pdb=" C ARG A1333 " pdb=" CB ARG A1333 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA ASN A 675 " pdb=" N ASN A 675 " pdb=" C ASN A 675 " pdb=" CB ASN A 675 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 1849 not shown) Planarity restraints: 2107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 398 " 0.031 2.00e-02 2.50e+03 6.09e-02 3.70e+01 pdb=" C PHE B 398 " -0.105 2.00e-02 2.50e+03 pdb=" O PHE B 398 " 0.039 2.00e-02 2.50e+03 pdb=" N GLY B 399 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1408 " 0.028 2.00e-02 2.50e+03 5.36e-02 2.87e+01 pdb=" C VAL A1408 " -0.093 2.00e-02 2.50e+03 pdb=" O VAL A1408 " 0.034 2.00e-02 2.50e+03 pdb=" N GLU A1409 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 142 " 0.029 2.00e-02 2.50e+03 3.24e-02 2.62e+01 pdb=" CG TRP B 142 " -0.083 2.00e-02 2.50e+03 pdb=" CD1 TRP B 142 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP B 142 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP B 142 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 142 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 142 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 142 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 142 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 142 " -0.001 2.00e-02 2.50e+03 ... (remaining 2104 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 221 2.67 - 3.22: 11166 3.22 - 3.78: 19714 3.78 - 4.34: 26724 4.34 - 4.90: 42883 Nonbonded interactions: 100708 Sorted by model distance: nonbonded pdb=" O3G ACP A1601 " pdb="MG MG A1602 " model vdw 2.107 2.170 nonbonded pdb=" O THR A 669 " pdb=" OG1 THR A 673 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR A1193 " pdb=" OE1 GLN A1280 " model vdw 2.220 3.040 nonbonded pdb=" O THR A1353 " pdb=" OG SER A1357 " model vdw 2.251 3.040 nonbonded pdb=" OG SER A1106 " pdb=" OE1 GLN A1109 " model vdw 2.273 3.040 ... (remaining 100703 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: 2.200 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.620 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: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 0.009 0.098 12263 Z= 0.400 Angle : 1.177 15.106 16647 Z= 0.624 Chirality : 0.067 0.348 1852 Planarity : 0.007 0.061 2106 Dihedral : 11.524 143.034 4438 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.38 % Favored : 91.55 % Rotamer: Outliers : 0.54 % Allowed : 3.79 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -5.16 (0.16), residues: 1480 helix: -4.19 (0.10), residues: 558 sheet: -2.77 (0.35), residues: 165 loop : -2.93 (0.19), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A1104 TYR 0.053 0.004 TYR A1217 PHE 0.051 0.004 PHE B 243 TRP 0.083 0.005 TRP B 142 HIS 0.013 0.002 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00931 / 0.40 (12258) covalent geometry : angle 1.16567 / 0.62 (16634) SS BOND : bond 0.01163 / 0.78 ( 2) SS BOND : angle 1.91428 / 1.51 ( 4) hydrogen bonds : bond 0.26942 / 17.42 ( 409) hydrogen bonds : angle 11.01811 / 7.61 ( 1125) link_BETA1-4 : bond 0.01346 / 0.91 ( 2) link_BETA1-4 : angle 7.02035 / 4.79 ( 6) link_NAG-ASN : bond 0.03246 / 2.16 ( 1) link_NAG-ASN : angle 7.14874 / 4.49 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 227 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 SER cc_start: 0.6782 (t) cc_final: 0.6492 (p) REVERT: A 265 ARG cc_start: 0.6690 (tpt-90) cc_final: 0.6443 (tpt-90) REVERT: A 485 MET cc_start: -0.0067 (ppp) cc_final: -0.0306 (ttp) REVERT: A 532 MET cc_start: 0.1316 (mtt) cc_final: 0.0144 (tpp) REVERT: A 561 PHE cc_start: 0.7455 (m-80) cc_final: 0.6765 (t80) REVERT: A 562 ILE cc_start: 0.8525 (mm) cc_final: 0.8299 (mt) REVERT: A 903 TYR cc_start: 0.6586 (m-10) cc_final: 0.6327 (m-10) REVERT: A 906 GLU cc_start: 0.6525 (pt0) cc_final: 0.6232 (pt0) REVERT: A 1006 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7913 (pp) REVERT: A 1044 TYR cc_start: 0.7883 (m-80) cc_final: 0.7667 (m-80) REVERT: A 1068 TYR cc_start: 0.8119 (m-80) cc_final: 0.7806 (m-10) REVERT: A 1088 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7665 (mtp180) REVERT: A 1196 MET cc_start: 0.8197 (tpp) cc_final: 0.7988 (mmm) REVERT: B 188 ARG cc_start: 0.7343 (ttt180) cc_final: 0.6852 (ttp-170) REVERT: B 315 MET cc_start: 0.8751 (mmm) cc_final: 0.8490 (mmm) outliers start: 7 outliers final: 3 residues processed: 233 average time/residue: 0.1238 time to fit residues: 40.7180 Evaluate side-chains 142 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 248 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 HIS A 597 ASN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 ASN A 736 ASN A 738 GLN ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1004 ASN A1139 GLN A1176 HIS A1307 HIS A1331 GLN A1419 HIS B 67 ASN B 155 GLN ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.193310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.140773 restraints weight = 14400.887| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.71 r_work: 0.3301 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12263 Z= 0.176 Angle : 0.739 12.682 16647 Z= 0.378 Chirality : 0.047 0.175 1852 Planarity : 0.005 0.053 2106 Dihedral : 7.742 138.820 1635 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.01 % Allowed : 8.44 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.73 (0.19), residues: 1480 helix: -2.34 (0.17), residues: 563 sheet: -2.77 (0.35), residues: 161 loop : -2.49 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 809 TYR 0.026 0.002 TYR A1219 PHE 0.023 0.002 PHE A 679 TRP 0.034 0.002 TRP B 142 HIS 0.004 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (12258) covalent geometry : angle 0.73323 / 0.38 (16634) SS BOND : bond 0.00318 / 0.21 ( 2) SS BOND : angle 0.46198 / 0.33 ( 4) hydrogen bonds : bond 0.04665 / 3.01 ( 409) hydrogen bonds : angle 6.26049 / 4.28 ( 1125) link_BETA1-4 : bond 0.00274 / 0.20 ( 2) link_BETA1-4 : angle 3.54598 / 2.51 ( 6) link_NAG-ASN : bond 0.01197 / 0.80 ( 1) link_NAG-ASN : angle 5.20668 / 4.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 263 SER cc_start: 0.6477 (t) cc_final: 0.6145 (p) REVERT: A 485 MET cc_start: -0.0202 (ppp) cc_final: -0.0512 (ttp) REVERT: A 519 MET cc_start: 0.4228 (mtt) cc_final: 0.2542 (mmt) REVERT: A 532 MET cc_start: 0.1482 (mtt) cc_final: 0.0364 (mmp) REVERT: A 561 PHE cc_start: 0.7668 (m-80) cc_final: 0.6828 (t80) REVERT: A 585 TYR cc_start: 0.8749 (m-80) cc_final: 0.7611 (m-80) REVERT: A 691 ARG cc_start: 0.6927 (ttp-170) cc_final: 0.6198 (tpp-160) REVERT: A 740 TYR cc_start: 0.6015 (p90) cc_final: 0.4617 (p90) REVERT: A 847 LYS cc_start: 0.6611 (mttt) cc_final: 0.5817 (mttt) REVERT: A 871 LYS cc_start: 0.8322 (ttpt) cc_final: 0.8017 (tttp) REVERT: A 901 GLU cc_start: 0.7043 (tp30) cc_final: 0.6736 (tp30) REVERT: A 994 GLU cc_start: 0.6878 (tp30) cc_final: 0.6645 (mm-30) REVERT: A 1004 ASN cc_start: 0.7562 (OUTLIER) cc_final: 0.7197 (t0) REVERT: A 1006 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7814 (pp) REVERT: A 1059 LYS cc_start: 0.6891 (ptpp) cc_final: 0.6651 (ptmt) REVERT: A 1088 ARG cc_start: 0.7521 (mtm-85) cc_final: 0.7321 (mtm-85) REVERT: A 1196 MET cc_start: 0.8614 (tpp) cc_final: 0.8366 (mmm) outliers start: 26 outliers final: 13 residues processed: 169 average time/residue: 0.1103 time to fit residues: 27.2652 Evaluate side-chains 137 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 966 ARG Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1212 ASP Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 53 optimal weight: 0.0170 chunk 74 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 18 optimal weight: 0.0070 chunk 147 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 41 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1004 ASN B 265 ASN ** B 366 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 = 0.4256 r_free = 0.4256 target = 0.194714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.143346 restraints weight = 14476.474| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.34 r_work: 0.3315 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12263 Z= 0.137 Angle : 0.651 11.247 16647 Z= 0.332 Chirality : 0.045 0.162 1852 Planarity : 0.004 0.045 2106 Dihedral : 7.199 135.649 1635 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.71 % Allowed : 9.21 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.96 (0.20), residues: 1480 helix: -1.39 (0.20), residues: 570 sheet: -2.51 (0.36), residues: 161 loop : -2.29 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 809 TYR 0.027 0.002 TYR A1219 PHE 0.014 0.002 PHE A1090 TRP 0.020 0.002 TRP B 142 HIS 0.003 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (12258) covalent geometry : angle 0.64463 / 0.33 (16634) SS BOND : bond 0.00225 / 0.15 ( 2) SS BOND : angle 0.64100 / 0.53 ( 4) hydrogen bonds : bond 0.04008 / 2.57 ( 409) hydrogen bonds : angle 5.60846 / 3.81 ( 1125) link_BETA1-4 : bond 0.00221 / 0.16 ( 2) link_BETA1-4 : angle 3.26194 / 2.29 ( 6) link_NAG-ASN : bond 0.01241 / 0.83 ( 1) link_NAG-ASN : angle 5.37839 / 4.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.458 Fit side-chains REVERT: A 266 THR cc_start: 0.5297 (t) cc_final: 0.5076 (p) REVERT: A 519 MET cc_start: 0.3720 (mtt) cc_final: 0.2182 (mmt) REVERT: A 532 MET cc_start: 0.1470 (mtt) cc_final: 0.0317 (mmp) REVERT: A 561 PHE cc_start: 0.7878 (m-80) cc_final: 0.6719 (t80) REVERT: A 585 TYR cc_start: 0.8676 (m-80) cc_final: 0.7786 (m-80) REVERT: A 691 ARG cc_start: 0.6790 (ttp-170) cc_final: 0.6093 (tpp-160) REVERT: A 730 LEU cc_start: 0.2478 (OUTLIER) cc_final: 0.1528 (mt) REVERT: A 1006 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7551 (pp) REVERT: A 1059 LYS cc_start: 0.6852 (ptpp) cc_final: 0.6567 (ptmt) REVERT: A 1100 VAL cc_start: 0.7893 (t) cc_final: 0.7658 (t) REVERT: A 1196 MET cc_start: 0.8669 (tpp) cc_final: 0.8355 (mmm) REVERT: A 1212 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8342 (t70) REVERT: B 269 ASP cc_start: 0.8288 (t0) cc_final: 0.8022 (t70) REVERT: B 359 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8674 (pt) outliers start: 35 outliers final: 17 residues processed: 156 average time/residue: 0.0945 time to fit residues: 21.7281 Evaluate side-chains 136 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1212 ASP Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 55 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 120 optimal weight: 0.0270 chunk 124 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 81 optimal weight: 0.0070 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.0470 chunk 142 optimal weight: 0.0010 chunk 28 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 overall best weight: 0.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.198560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.146793 restraints weight = 14424.131| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.93 r_work: 0.3359 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12263 Z= 0.115 Angle : 0.616 10.273 16647 Z= 0.315 Chirality : 0.044 0.162 1852 Planarity : 0.004 0.042 2106 Dihedral : 6.849 134.896 1635 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.55 % Allowed : 10.84 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.54 (0.21), residues: 1480 helix: -0.92 (0.21), residues: 570 sheet: -2.35 (0.37), residues: 172 loop : -2.13 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 809 TYR 0.024 0.001 TYR A1219 PHE 0.013 0.001 PHE A 834 TRP 0.015 0.001 TRP A 517 HIS 0.002 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (12258) covalent geometry : angle 0.61024 / 0.31 (16634) SS BOND : bond 0.00172 / 0.12 ( 2) SS BOND : angle 0.46527 / 0.35 ( 4) hydrogen bonds : bond 0.03546 / 2.28 ( 409) hydrogen bonds : angle 5.34189 / 3.62 ( 1125) link_BETA1-4 : bond 0.00357 / 0.26 ( 2) link_BETA1-4 : angle 3.09442 / 2.14 ( 6) link_NAG-ASN : bond 0.00807 / 0.54 ( 1) link_NAG-ASN : angle 4.96159 / 3.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.329 Fit side-chains REVERT: A 224 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8237 (tm) REVERT: A 266 THR cc_start: 0.5600 (t) cc_final: 0.5340 (p) REVERT: A 519 MET cc_start: 0.3780 (mtt) cc_final: 0.2254 (mmt) REVERT: A 532 MET cc_start: 0.1553 (mtt) cc_final: 0.0339 (mmp) REVERT: A 561 PHE cc_start: 0.7686 (m-80) cc_final: 0.6804 (t80) REVERT: A 585 TYR cc_start: 0.8574 (m-80) cc_final: 0.7911 (m-80) REVERT: A 691 ARG cc_start: 0.6614 (ttp-170) cc_final: 0.5921 (tpp-160) REVERT: A 730 LEU cc_start: 0.2085 (OUTLIER) cc_final: 0.1293 (mt) REVERT: A 847 LYS cc_start: 0.6144 (mttt) cc_final: 0.5426 (mttt) REVERT: A 1006 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7257 (pp) REVERT: A 1059 LYS cc_start: 0.6874 (ptpp) cc_final: 0.6614 (ptmt) REVERT: A 1100 VAL cc_start: 0.7817 (t) cc_final: 0.7587 (t) REVERT: A 1196 MET cc_start: 0.8595 (tpp) cc_final: 0.8219 (mmm) REVERT: B 269 ASP cc_start: 0.8285 (t0) cc_final: 0.8043 (t70) REVERT: B 315 MET cc_start: 0.8817 (mmm) cc_final: 0.8575 (mmm) REVERT: B 359 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8493 (pt) outliers start: 33 outliers final: 19 residues processed: 152 average time/residue: 0.0993 time to fit residues: 22.7462 Evaluate side-chains 133 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1212 ASP Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 0.0670 chunk 52 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 GLN A1004 ASN A1331 GLN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.195312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.131215 restraints weight = 14417.873| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.60 r_work: 0.3337 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12263 Z= 0.159 Angle : 0.642 11.831 16647 Z= 0.324 Chirality : 0.045 0.161 1852 Planarity : 0.004 0.044 2106 Dihedral : 6.797 136.110 1635 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.09 % Allowed : 11.84 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.37 (0.21), residues: 1480 helix: -0.78 (0.21), residues: 579 sheet: -2.12 (0.39), residues: 162 loop : -2.09 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 809 TYR 0.022 0.002 TYR B 280 PHE 0.015 0.002 PHE B 353 TRP 0.019 0.001 TRP A 986 HIS 0.003 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (12258) covalent geometry : angle 0.63542 / 0.32 (16634) SS BOND : bond 0.00211 / 0.14 ( 2) SS BOND : angle 0.76129 / 0.58 ( 4) hydrogen bonds : bond 0.03671 / 2.38 ( 409) hydrogen bonds : angle 5.23410 / 3.56 ( 1125) link_BETA1-4 : bond 0.00366 / 0.25 ( 2) link_BETA1-4 : angle 3.29552 / 2.31 ( 6) link_NAG-ASN : bond 0.01542 / 1.03 ( 1) link_NAG-ASN : angle 4.99381 / 3.93 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.456 Fit side-chains REVERT: A 224 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8370 (tm) REVERT: A 519 MET cc_start: 0.4025 (mtt) cc_final: 0.2211 (mmt) REVERT: A 532 MET cc_start: 0.1608 (mtt) cc_final: 0.0147 (mmm) REVERT: A 561 PHE cc_start: 0.7792 (m-80) cc_final: 0.6784 (t80) REVERT: A 585 TYR cc_start: 0.8817 (m-80) cc_final: 0.7766 (m-80) REVERT: A 603 TRP cc_start: 0.8403 (m100) cc_final: 0.8001 (m100) REVERT: A 691 ARG cc_start: 0.6735 (ttp-170) cc_final: 0.6067 (tpp-160) REVERT: A 730 LEU cc_start: 0.2389 (OUTLIER) cc_final: 0.1492 (mt) REVERT: A 795 LYS cc_start: 0.7401 (mmtm) cc_final: 0.7042 (mmtm) REVERT: A 847 LYS cc_start: 0.6316 (mttt) cc_final: 0.5537 (mttt) REVERT: A 1006 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7433 (pp) REVERT: A 1196 MET cc_start: 0.8727 (tpp) cc_final: 0.8342 (mmm) REVERT: A 1212 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8338 (t70) REVERT: B 80 LEU cc_start: 0.7440 (tt) cc_final: 0.7105 (tp) outliers start: 27 outliers final: 20 residues processed: 137 average time/residue: 0.0981 time to fit residues: 20.5387 Evaluate side-chains 131 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 966 ARG Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1212 ASP Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 58 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.194433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.141844 restraints weight = 14502.604| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.29 r_work: 0.3284 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12263 Z= 0.170 Angle : 0.642 11.612 16647 Z= 0.326 Chirality : 0.046 0.167 1852 Planarity : 0.004 0.043 2106 Dihedral : 6.834 140.971 1635 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.79 % Allowed : 11.92 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.23 (0.21), residues: 1480 helix: -0.69 (0.21), residues: 585 sheet: -1.99 (0.40), residues: 163 loop : -2.01 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 809 TYR 0.022 0.002 TYR B 280 PHE 0.013 0.002 PHE A1224 TRP 0.021 0.001 TRP A 986 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (12258) covalent geometry : angle 0.63606 / 0.32 (16634) SS BOND : bond 0.00233 / 0.16 ( 2) SS BOND : angle 0.81335 / 0.62 ( 4) hydrogen bonds : bond 0.03722 / 2.42 ( 409) hydrogen bonds : angle 5.16965 / 3.51 ( 1125) link_BETA1-4 : bond 0.00249 / 0.17 ( 2) link_BETA1-4 : angle 3.32519 / 2.31 ( 6) link_NAG-ASN : bond 0.01690 / 1.13 ( 1) link_NAG-ASN : angle 4.88559 / 3.81 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 0.351 Fit side-chains REVERT: A 223 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.8105 (t80) REVERT: A 224 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8382 (tm) REVERT: A 519 MET cc_start: 0.3772 (mtt) cc_final: 0.2269 (mmt) REVERT: A 532 MET cc_start: 0.1620 (mtt) cc_final: 0.0132 (mmm) REVERT: A 561 PHE cc_start: 0.7747 (m-80) cc_final: 0.6784 (t80) REVERT: A 691 ARG cc_start: 0.6529 (ttp-170) cc_final: 0.5894 (tpp-160) REVERT: A 730 LEU cc_start: 0.2328 (OUTLIER) cc_final: 0.1425 (mt) REVERT: A 795 LYS cc_start: 0.7394 (mmtm) cc_final: 0.7035 (mmtm) REVERT: A 847 LYS cc_start: 0.6328 (mttt) cc_final: 0.5552 (mttt) REVERT: A 1006 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7463 (pp) REVERT: A 1055 PHE cc_start: 0.5081 (OUTLIER) cc_final: 0.4599 (m-80) REVERT: A 1196 MET cc_start: 0.8601 (tpp) cc_final: 0.8370 (mmm) REVERT: A 1212 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8309 (t70) REVERT: B 80 LEU cc_start: 0.7473 (tt) cc_final: 0.7167 (tp) REVERT: B 395 PHE cc_start: 0.7321 (m-80) cc_final: 0.7019 (m-10) outliers start: 36 outliers final: 24 residues processed: 138 average time/residue: 0.0955 time to fit residues: 20.0352 Evaluate side-chains 130 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 966 ARG Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1212 ASP Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 118 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 133 optimal weight: 0.0050 chunk 36 optimal weight: 0.6980 chunk 143 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 484 ASN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.194326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.142722 restraints weight = 14371.963| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.25 r_work: 0.3254 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12263 Z= 0.157 Angle : 0.632 10.339 16647 Z= 0.320 Chirality : 0.045 0.160 1852 Planarity : 0.003 0.038 2106 Dihedral : 6.800 142.179 1635 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.79 % Allowed : 11.84 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.17 (0.21), residues: 1480 helix: -0.69 (0.21), residues: 596 sheet: -1.86 (0.41), residues: 162 loop : -1.96 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 809 TYR 0.023 0.002 TYR B 280 PHE 0.013 0.002 PHE B 353 TRP 0.019 0.001 TRP A 986 HIS 0.004 0.001 HIS A1330 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (12258) covalent geometry : angle 0.62591 / 0.32 (16634) SS BOND : bond 0.00228 / 0.16 ( 2) SS BOND : angle 0.76802 / 0.57 ( 4) hydrogen bonds : bond 0.03665 / 2.38 ( 409) hydrogen bonds : angle 5.10986 / 3.47 ( 1125) link_BETA1-4 : bond 0.00210 / 0.14 ( 2) link_BETA1-4 : angle 3.29005 / 2.27 ( 6) link_NAG-ASN : bond 0.01540 / 1.03 ( 1) link_NAG-ASN : angle 4.85300 / 3.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.358 Fit side-chains REVERT: A 223 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.8186 (t80) REVERT: A 224 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8352 (tm) REVERT: A 519 MET cc_start: 0.3373 (mtt) cc_final: 0.2117 (mmt) REVERT: A 532 MET cc_start: 0.1687 (mtt) cc_final: 0.0196 (mmt) REVERT: A 561 PHE cc_start: 0.7756 (m-80) cc_final: 0.6792 (t80) REVERT: A 603 TRP cc_start: 0.8356 (m100) cc_final: 0.8112 (m100) REVERT: A 691 ARG cc_start: 0.6576 (ttp-170) cc_final: 0.5928 (tpp-160) REVERT: A 730 LEU cc_start: 0.2480 (OUTLIER) cc_final: 0.1538 (mt) REVERT: A 795 LYS cc_start: 0.7496 (mmtm) cc_final: 0.7144 (mmtm) REVERT: A 847 LYS cc_start: 0.6326 (mttt) cc_final: 0.5565 (mttt) REVERT: A 1006 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7603 (pp) REVERT: A 1055 PHE cc_start: 0.5171 (OUTLIER) cc_final: 0.4659 (m-80) REVERT: A 1196 MET cc_start: 0.8610 (tpp) cc_final: 0.8388 (mmm) REVERT: A 1212 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8333 (t70) REVERT: B 395 PHE cc_start: 0.7356 (m-80) cc_final: 0.7043 (m-10) outliers start: 36 outliers final: 29 residues processed: 134 average time/residue: 0.0932 time to fit residues: 18.9542 Evaluate side-chains 133 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 966 ARG Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1212 ASP Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.0030 chunk 102 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 106 optimal weight: 0.5980 chunk 93 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 138 optimal weight: 0.5980 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 ASN ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.196034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.143870 restraints weight = 14350.053| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 3.11 r_work: 0.3306 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12263 Z= 0.131 Angle : 0.608 8.384 16647 Z= 0.308 Chirality : 0.044 0.159 1852 Planarity : 0.003 0.034 2106 Dihedral : 6.657 141.303 1635 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.63 % Allowed : 12.38 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.03 (0.21), residues: 1480 helix: -0.55 (0.21), residues: 598 sheet: -1.69 (0.41), residues: 161 loop : -1.93 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 264 TYR 0.023 0.002 TYR A 633 PHE 0.016 0.001 PHE A1402 TRP 0.018 0.001 TRP A 986 HIS 0.003 0.001 HIS A1330 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (12258) covalent geometry : angle 0.60171 / 0.31 (16634) SS BOND : bond 0.00172 / 0.12 ( 2) SS BOND : angle 0.69906 / 0.51 ( 4) hydrogen bonds : bond 0.03469 / 2.25 ( 409) hydrogen bonds : angle 5.00354 / 3.39 ( 1125) link_BETA1-4 : bond 0.00224 / 0.16 ( 2) link_BETA1-4 : angle 3.16811 / 2.19 ( 6) link_NAG-ASN : bond 0.01142 / 0.76 ( 1) link_NAG-ASN : angle 4.74679 / 3.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.363 Fit side-chains REVERT: A 223 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.8096 (t80) REVERT: A 224 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8375 (tm) REVERT: A 519 MET cc_start: 0.3607 (mtt) cc_final: 0.2380 (mmt) REVERT: A 532 MET cc_start: 0.1678 (mtt) cc_final: 0.0211 (mmt) REVERT: A 561 PHE cc_start: 0.7635 (m-80) cc_final: 0.6710 (t80) REVERT: A 585 TYR cc_start: 0.8707 (m-80) cc_final: 0.7793 (m-80) REVERT: A 603 TRP cc_start: 0.8297 (m100) cc_final: 0.8066 (m100) REVERT: A 691 ARG cc_start: 0.6432 (ttp-170) cc_final: 0.5770 (tpp-160) REVERT: A 730 LEU cc_start: 0.2301 (OUTLIER) cc_final: 0.1384 (mt) REVERT: A 801 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: A 814 SER cc_start: 0.6341 (t) cc_final: 0.5535 (p) REVERT: A 847 LYS cc_start: 0.6168 (mttt) cc_final: 0.5461 (mttt) REVERT: A 1006 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7546 (pp) REVERT: A 1055 PHE cc_start: 0.4853 (OUTLIER) cc_final: 0.4351 (m-80) REVERT: A 1118 LYS cc_start: 0.7827 (ttpp) cc_final: 0.7619 (ttpp) REVERT: A 1212 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8266 (t70) REVERT: A 1219 TYR cc_start: 0.8345 (t80) cc_final: 0.7731 (t80) REVERT: B 80 LEU cc_start: 0.7476 (tt) cc_final: 0.7050 (tp) REVERT: B 351 LEU cc_start: 0.8391 (mt) cc_final: 0.8168 (mt) REVERT: B 395 PHE cc_start: 0.7404 (m-80) cc_final: 0.7104 (m-10) outliers start: 34 outliers final: 21 residues processed: 140 average time/residue: 0.0832 time to fit residues: 17.9337 Evaluate side-chains 129 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1212 ASP Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 9 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 71 optimal weight: 0.0270 chunk 88 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 111 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 504 ASN ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.194858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.142792 restraints weight = 14324.616| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.02 r_work: 0.3291 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12263 Z= 0.141 Angle : 0.610 7.419 16647 Z= 0.309 Chirality : 0.044 0.157 1852 Planarity : 0.003 0.040 2106 Dihedral : 6.675 142.699 1635 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.55 % Allowed : 12.77 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.00 (0.21), residues: 1480 helix: -0.51 (0.21), residues: 603 sheet: -1.64 (0.42), residues: 161 loop : -1.95 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 264 TYR 0.024 0.002 TYR A 903 PHE 0.013 0.001 PHE A1402 TRP 0.019 0.001 TRP A 986 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (12258) covalent geometry : angle 0.60373 / 0.31 (16634) SS BOND : bond 0.00178 / 0.12 ( 2) SS BOND : angle 0.74890 / 0.55 ( 4) hydrogen bonds : bond 0.03476 / 2.27 ( 409) hydrogen bonds : angle 4.98589 / 3.38 ( 1125) link_BETA1-4 : bond 0.00206 / 0.14 ( 2) link_BETA1-4 : angle 3.25279 / 2.26 ( 6) link_NAG-ASN : bond 0.01314 / 0.88 ( 1) link_NAG-ASN : angle 4.84382 / 3.84 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.447 Fit side-chains REVERT: A 223 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.8130 (t80) REVERT: A 224 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8388 (tm) REVERT: A 519 MET cc_start: 0.3485 (mtt) cc_final: 0.2549 (mmt) REVERT: A 532 MET cc_start: 0.1714 (mtt) cc_final: 0.0202 (mmt) REVERT: A 561 PHE cc_start: 0.7581 (m-80) cc_final: 0.6685 (t80) REVERT: A 603 TRP cc_start: 0.8271 (m100) cc_final: 0.8034 (m100) REVERT: A 691 ARG cc_start: 0.6457 (ttp-170) cc_final: 0.5729 (tpp-160) REVERT: A 730 LEU cc_start: 0.2361 (OUTLIER) cc_final: 0.1413 (mt) REVERT: A 795 LYS cc_start: 0.7363 (mmtm) cc_final: 0.6928 (mmtm) REVERT: A 801 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7534 (tt0) REVERT: A 814 SER cc_start: 0.6177 (t) cc_final: 0.5430 (p) REVERT: A 847 LYS cc_start: 0.5936 (mttt) cc_final: 0.5276 (mttt) REVERT: A 1006 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7546 (pp) REVERT: A 1055 PHE cc_start: 0.4746 (OUTLIER) cc_final: 0.4204 (m-80) REVERT: A 1059 LYS cc_start: 0.7090 (ptpp) cc_final: 0.6731 (ptmt) REVERT: A 1092 LEU cc_start: 0.8267 (mp) cc_final: 0.8041 (tp) REVERT: A 1118 LYS cc_start: 0.7871 (ttpp) cc_final: 0.7646 (ttpp) REVERT: A 1120 SER cc_start: 0.9144 (m) cc_final: 0.8357 (t) REVERT: A 1212 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8296 (t70) REVERT: A 1219 TYR cc_start: 0.8375 (t80) cc_final: 0.7666 (t80) REVERT: B 80 LEU cc_start: 0.7534 (tt) cc_final: 0.7148 (tp) REVERT: B 351 LEU cc_start: 0.8350 (mt) cc_final: 0.8130 (mt) REVERT: B 395 PHE cc_start: 0.7496 (m-80) cc_final: 0.7184 (m-10) outliers start: 33 outliers final: 22 residues processed: 133 average time/residue: 0.0851 time to fit residues: 17.3314 Evaluate side-chains 136 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 966 ARG Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1212 ASP Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.191684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.139644 restraints weight = 14463.890| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 3.03 r_work: 0.3242 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12263 Z= 0.190 Angle : 0.654 8.011 16647 Z= 0.331 Chirality : 0.046 0.178 1852 Planarity : 0.004 0.045 2106 Dihedral : 6.830 143.322 1635 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.40 % Allowed : 12.77 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.02 (0.21), residues: 1480 helix: -0.57 (0.21), residues: 603 sheet: -1.61 (0.42), residues: 160 loop : -1.93 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 264 TYR 0.029 0.002 TYR A 903 PHE 0.030 0.002 PHE A1402 TRP 0.027 0.002 TRP A 986 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (12258) covalent geometry : angle 0.64689 / 0.33 (16634) SS BOND : bond 0.00256 / 0.17 ( 2) SS BOND : angle 0.94935 / 0.70 ( 4) hydrogen bonds : bond 0.03752 / 2.46 ( 409) hydrogen bonds : angle 5.04517 / 3.43 ( 1125) link_BETA1-4 : bond 0.00351 / 0.23 ( 2) link_BETA1-4 : angle 3.47662 / 2.44 ( 6) link_NAG-ASN : bond 0.01757 / 1.17 ( 1) link_NAG-ASN : angle 5.02299 / 4.00 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.453 Fit side-chains REVERT: A 223 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.8089 (t80) REVERT: A 224 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8450 (tm) REVERT: A 519 MET cc_start: 0.3487 (mtt) cc_final: 0.2562 (mmt) REVERT: A 532 MET cc_start: 0.1888 (mtt) cc_final: 0.0341 (mmt) REVERT: A 561 PHE cc_start: 0.7722 (m-80) cc_final: 0.6757 (t80) REVERT: A 603 TRP cc_start: 0.8285 (m100) cc_final: 0.8041 (m100) REVERT: A 691 ARG cc_start: 0.6454 (ttp-170) cc_final: 0.5781 (tpp-160) REVERT: A 795 LYS cc_start: 0.7444 (mmtm) cc_final: 0.6999 (mmtm) REVERT: A 801 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: A 814 SER cc_start: 0.6269 (t) cc_final: 0.5522 (p) REVERT: A 847 LYS cc_start: 0.5999 (mttt) cc_final: 0.5464 (mttm) REVERT: A 1006 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7630 (pp) REVERT: A 1055 PHE cc_start: 0.4852 (OUTLIER) cc_final: 0.4280 (m-80) REVERT: A 1092 LEU cc_start: 0.8307 (mp) cc_final: 0.8033 (tp) REVERT: A 1120 SER cc_start: 0.9214 (m) cc_final: 0.8949 (m) REVERT: A 1196 MET cc_start: 0.8643 (tpp) cc_final: 0.8364 (mmm) REVERT: A 1212 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8278 (t70) REVERT: A 1219 TYR cc_start: 0.8401 (t80) cc_final: 0.7791 (t80) REVERT: B 80 LEU cc_start: 0.7570 (tt) cc_final: 0.7190 (tp) REVERT: B 333 ASP cc_start: 0.7496 (t0) cc_final: 0.7294 (t0) REVERT: B 395 PHE cc_start: 0.7775 (m-80) cc_final: 0.7393 (m-10) outliers start: 31 outliers final: 24 residues processed: 136 average time/residue: 0.0961 time to fit residues: 20.0959 Evaluate side-chains 138 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 966 ARG Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1212 ASP Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 146 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 134 optimal weight: 0.0170 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.192442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.141259 restraints weight = 14340.355| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.94 r_work: 0.3277 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12263 Z= 0.161 Angle : 0.637 10.265 16647 Z= 0.321 Chirality : 0.045 0.162 1852 Planarity : 0.003 0.039 2106 Dihedral : 6.775 142.980 1635 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.48 % Allowed : 12.93 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.97 (0.22), residues: 1480 helix: -0.53 (0.21), residues: 604 sheet: -1.56 (0.42), residues: 159 loop : -1.90 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 264 TYR 0.033 0.002 TYR A 903 PHE 0.015 0.002 PHE A1402 TRP 0.021 0.001 TRP A 986 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (12258) covalent geometry : angle 0.63049 / 0.32 (16634) SS BOND : bond 0.00269 / 0.19 ( 2) SS BOND : angle 0.85702 / 0.63 ( 4) hydrogen bonds : bond 0.03640 / 2.38 ( 409) hydrogen bonds : angle 5.01067 / 3.40 ( 1125) link_BETA1-4 : bond 0.00212 / 0.14 ( 2) link_BETA1-4 : angle 3.35785 / 2.33 ( 6) link_NAG-ASN : bond 0.01418 / 0.95 ( 1) link_NAG-ASN : angle 4.79694 / 3.81 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3154.01 seconds wall clock time: 54 minutes 50.87 seconds (3290.87 seconds total)