Starting phenix.real_space_refine on Wed Jun 11 02:51:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7whw_32513/06_2025/7whw_32513.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whw_32513/06_2025/7whw_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_32513/06_2025/7whw_32513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whw_32513/06_2025/7whw_32513.map" model { file = "/net/cci-nas-00/data/ceres_data/7whw_32513/06_2025/7whw_32513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whw_32513/06_2025/7whw_32513.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 9 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: 7.55, per 1000 atoms: 0.63 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: 3.37 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.39 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: 4.56 Time building geometry restraints manager: 3.52 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: 7121 28.61 - 57.21: 174 57.21 - 85.82: 14 85.82 - 114.43: 5 114.43 - 143.03: 1 Dihedral angle restraints: 7315 sinusoidal: 2977 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 7312 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: 2.750 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: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.730 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 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 : 12.722 143.034 4527 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.84 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.083 0.005 TRP B 142 HIS 0.013 0.002 HIS B 186 PHE 0.051 0.004 PHE B 243 TYR 0.053 0.004 TYR A1217 ARG 0.021 0.001 ARG A1104 Details of bonding type rmsd link_NAG-ASN : bond 0.03246 ( 1) link_NAG-ASN : angle 7.14874 ( 3) link_BETA1-4 : bond 0.01346 ( 2) link_BETA1-4 : angle 7.02035 ( 6) hydrogen bonds : bond 0.26942 ( 409) hydrogen bonds : angle 11.01811 ( 1125) SS BOND : bond 0.01163 ( 2) SS BOND : angle 1.91428 ( 4) covalent geometry : bond 0.00931 (12258) covalent geometry : angle 1.16567 (16634) *********************** 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 : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 SER cc_start: 0.6781 (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: 0.2716 time to fit residues: 88.4742 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 : 1.296 ------------------------------------------------------------------------------- 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 124 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 A1419 HIS B 67 ASN B 155 GLN ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.192310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.139451 restraints weight = 14272.211| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.73 r_work: 0.3288 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12263 Z= 0.197 Angle : 0.756 12.857 16647 Z= 0.386 Chirality : 0.048 0.172 1852 Planarity : 0.005 0.052 2106 Dihedral : 10.177 137.470 1724 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.09 % Allowed : 8.44 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.19), residues: 1480 helix: -2.32 (0.17), residues: 567 sheet: -2.90 (0.35), residues: 154 loop : -2.51 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 142 HIS 0.004 0.001 HIS B 125 PHE 0.022 0.002 PHE A 679 TYR 0.027 0.002 TYR A1219 ARG 0.009 0.001 ARG A 809 Details of bonding type rmsd link_NAG-ASN : bond 0.01834 ( 1) link_NAG-ASN : angle 6.12957 ( 3) link_BETA1-4 : bond 0.00419 ( 2) link_BETA1-4 : angle 4.13281 ( 6) hydrogen bonds : bond 0.04580 ( 409) hydrogen bonds : angle 6.17992 ( 1125) SS BOND : bond 0.00355 ( 2) SS BOND : angle 0.53933 ( 4) covalent geometry : bond 0.00446 (12258) covalent geometry : angle 0.74773 (16634) *********************** 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 175 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 SER cc_start: 0.6485 (t) cc_final: 0.6166 (p) REVERT: A 519 MET cc_start: 0.4518 (mtt) cc_final: 0.2859 (mmt) REVERT: A 532 MET cc_start: 0.1510 (mtt) cc_final: 0.0367 (mmp) REVERT: A 561 PHE cc_start: 0.7841 (m-80) cc_final: 0.6838 (t80) REVERT: A 691 ARG cc_start: 0.6964 (ttp-170) cc_final: 0.6256 (tpp-160) REVERT: A 847 LYS cc_start: 0.6718 (mttt) cc_final: 0.5916 (mttt) REVERT: A 871 LYS cc_start: 0.8337 (ttpt) cc_final: 0.8033 (tttp) REVERT: A 901 GLU cc_start: 0.7061 (tp30) cc_final: 0.6760 (tp30) REVERT: A 994 GLU cc_start: 0.6908 (tp30) cc_final: 0.6665 (mm-30) REVERT: A 1004 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7262 (t0) REVERT: A 1006 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7832 (pp) REVERT: A 1059 LYS cc_start: 0.6898 (ptpp) cc_final: 0.6656 (ptmt) REVERT: A 1196 MET cc_start: 0.8622 (tpp) cc_final: 0.8358 (mmm) outliers start: 27 outliers final: 13 residues processed: 167 average time/residue: 0.2632 time to fit residues: 63.8682 Evaluate side-chains 134 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 124 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 chunk 62 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1004 ASN B 265 ASN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4228 r_free = 0.4228 target = 0.191949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.140600 restraints weight = 14458.349| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.13 r_work: 0.3252 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2413 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= 0.181 Angle : 0.689 11.536 16647 Z= 0.350 Chirality : 0.047 0.164 1852 Planarity : 0.004 0.037 2106 Dihedral : 9.294 136.194 1724 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.20), residues: 1480 helix: -1.48 (0.19), residues: 578 sheet: -2.52 (0.36), residues: 162 loop : -2.29 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 142 HIS 0.004 0.001 HIS B 347 PHE 0.015 0.002 PHE A1090 TYR 0.026 0.002 TYR A1219 ARG 0.010 0.001 ARG A 264 Details of bonding type rmsd link_NAG-ASN : bond 0.01714 ( 1) link_NAG-ASN : angle 5.99493 ( 3) link_BETA1-4 : bond 0.00301 ( 2) link_BETA1-4 : angle 3.95947 ( 6) hydrogen bonds : bond 0.04200 ( 409) hydrogen bonds : angle 5.66421 ( 1125) SS BOND : bond 0.00293 ( 2) SS BOND : angle 0.81045 ( 4) covalent geometry : bond 0.00416 (12258) covalent geometry : angle 0.67994 (16634) *********************** 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 161 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 1.379 Fit side-chains REVERT: A 266 THR cc_start: 0.5355 (t) cc_final: 0.5104 (p) REVERT: A 519 MET cc_start: 0.4131 (mtt) cc_final: 0.2664 (mmt) REVERT: A 532 MET cc_start: 0.1573 (mtt) cc_final: 0.0336 (mmp) REVERT: A 561 PHE cc_start: 0.8005 (m-80) cc_final: 0.6773 (t80) REVERT: A 691 ARG cc_start: 0.6843 (ttp-170) cc_final: 0.6172 (tpp-160) REVERT: A 730 LEU cc_start: 0.2346 (OUTLIER) cc_final: 0.1462 (mt) REVERT: A 964 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6742 (tt0) REVERT: A 1006 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7666 (pp) REVERT: A 1059 LYS cc_start: 0.6883 (ptpp) cc_final: 0.6599 (ptmt) REVERT: A 1196 MET cc_start: 0.8693 (tpp) cc_final: 0.8347 (mmm) REVERT: A 1212 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8353 (t70) REVERT: B 269 ASP cc_start: 0.8360 (t0) cc_final: 0.8140 (t70) REVERT: B 359 ILE cc_start: 0.8961 (mt) cc_final: 0.8633 (pt) outliers start: 35 outliers final: 19 residues processed: 156 average time/residue: 0.2910 time to fit residues: 66.7064 Evaluate side-chains 128 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 1.435 ------------------------------------------------------------------------------- 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 964 GLU 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 80 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 14 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 51 optimal weight: 10.0000 chunk 12 optimal weight: 0.0870 chunk 59 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 GLN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.191925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.140092 restraints weight = 14327.753| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 3.86 r_work: 0.3253 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12263 Z= 0.171 Angle : 0.667 11.271 16647 Z= 0.340 Chirality : 0.046 0.161 1852 Planarity : 0.004 0.059 2106 Dihedral : 8.900 134.050 1724 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.79 % Allowed : 10.84 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.21), residues: 1480 helix: -1.09 (0.20), residues: 577 sheet: -2.39 (0.37), residues: 174 loop : -2.16 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 986 HIS 0.003 0.001 HIS B 347 PHE 0.014 0.002 PHE A1341 TYR 0.026 0.002 TYR A1219 ARG 0.004 0.000 ARG A 809 Details of bonding type rmsd link_NAG-ASN : bond 0.01588 ( 1) link_NAG-ASN : angle 5.79172 ( 3) link_BETA1-4 : bond 0.00378 ( 2) link_BETA1-4 : angle 3.77420 ( 6) hydrogen bonds : bond 0.03868 ( 409) hydrogen bonds : angle 5.47468 ( 1125) SS BOND : bond 0.00281 ( 2) SS BOND : angle 0.77886 ( 4) covalent geometry : bond 0.00393 (12258) covalent geometry : angle 0.65904 (16634) *********************** 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 150 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 1.301 Fit side-chains REVERT: A 224 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8293 (tm) REVERT: A 266 THR cc_start: 0.5514 (t) cc_final: 0.5246 (p) REVERT: A 519 MET cc_start: 0.3934 (mtt) cc_final: 0.2316 (mmt) REVERT: A 532 MET cc_start: 0.1525 (mtt) cc_final: 0.0101 (mmm) REVERT: A 561 PHE cc_start: 0.7920 (m-80) cc_final: 0.6781 (t80) REVERT: A 691 ARG cc_start: 0.6642 (ttp-170) cc_final: 0.5963 (tpp-160) REVERT: A 730 LEU cc_start: 0.2454 (OUTLIER) cc_final: 0.1548 (mt) REVERT: A 871 LYS cc_start: 0.7903 (ptpt) cc_final: 0.7661 (ptmm) REVERT: A 964 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6578 (tt0) REVERT: A 1006 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7376 (pp) REVERT: A 1059 LYS cc_start: 0.6867 (ptpp) cc_final: 0.6555 (ptmt) REVERT: A 1089 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8095 (mttm) REVERT: A 1100 VAL cc_start: 0.8036 (t) cc_final: 0.7815 (t) REVERT: A 1196 MET cc_start: 0.8653 (tpp) cc_final: 0.8303 (mmm) REVERT: A 1212 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8355 (t70) REVERT: B 359 ILE cc_start: 0.8941 (mt) cc_final: 0.8642 (pt) REVERT: B 395 PHE cc_start: 0.7390 (m-80) cc_final: 0.6972 (m-10) outliers start: 36 outliers final: 22 residues processed: 146 average time/residue: 0.3133 time to fit residues: 69.3208 Evaluate side-chains 134 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 1.459 ------------------------------------------------------------------------------- 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 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 964 GLU Chi-restraints excluded: chain A residue 966 ARG 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 1089 LYS 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 76 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 94 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 85 optimal weight: 0.0570 chunk 92 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 ASN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1004 ASN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.191007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.138763 restraints weight = 14397.520| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.52 r_work: 0.3253 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2878 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= 0.179 Angle : 0.658 10.784 16647 Z= 0.335 Chirality : 0.046 0.162 1852 Planarity : 0.004 0.054 2106 Dihedral : 8.656 138.026 1724 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.10 % Allowed : 11.22 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.21), residues: 1480 helix: -0.89 (0.21), residues: 583 sheet: -2.28 (0.37), residues: 172 loop : -2.09 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 986 HIS 0.004 0.001 HIS B 347 PHE 0.015 0.002 PHE A1341 TYR 0.026 0.002 TYR A1219 ARG 0.004 0.000 ARG A 809 Details of bonding type rmsd link_NAG-ASN : bond 0.01644 ( 1) link_NAG-ASN : angle 5.75075 ( 3) link_BETA1-4 : bond 0.00445 ( 2) link_BETA1-4 : angle 3.66270 ( 6) hydrogen bonds : bond 0.03821 ( 409) hydrogen bonds : angle 5.33699 ( 1125) SS BOND : bond 0.00308 ( 2) SS BOND : angle 0.80589 ( 4) covalent geometry : bond 0.00413 (12258) covalent geometry : angle 0.65028 (16634) *********************** 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 148 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 1.218 Fit side-chains REVERT: A 223 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8116 (t80) REVERT: A 224 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8419 (tm) REVERT: A 266 THR cc_start: 0.5499 (t) cc_final: 0.5274 (p) REVERT: A 519 MET cc_start: 0.3849 (mtt) cc_final: 0.2767 (mmt) REVERT: A 532 MET cc_start: 0.1609 (mtt) cc_final: 0.0097 (mmm) REVERT: A 561 PHE cc_start: 0.7901 (m-80) cc_final: 0.6780 (t80) REVERT: A 691 ARG cc_start: 0.6607 (ttp-170) cc_final: 0.5975 (tpp-160) REVERT: A 730 LEU cc_start: 0.2530 (OUTLIER) cc_final: 0.1619 (mt) REVERT: A 1006 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7621 (pp) REVERT: A 1059 LYS cc_start: 0.6946 (ptpp) cc_final: 0.6639 (ptmt) REVERT: A 1089 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8075 (mttm) REVERT: A 1196 MET cc_start: 0.8656 (tpp) cc_final: 0.8313 (mmm) REVERT: A 1212 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8348 (t70) REVERT: B 359 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8676 (pt) REVERT: B 395 PHE cc_start: 0.7556 (m-80) cc_final: 0.7067 (m-10) outliers start: 40 outliers final: 28 residues processed: 141 average time/residue: 0.2457 time to fit residues: 52.5686 Evaluate side-chains 137 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 1.304 ------------------------------------------------------------------------------- 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 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 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 1089 LYS Chi-restraints excluded: chain A residue 1095 LYS Chi-restraints excluded: chain A residue 1101 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 A residue 1353 THR 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 300 THR Chi-restraints excluded: chain B residue 359 ILE 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 85 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1004 ASN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.190526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.137728 restraints weight = 14632.240| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 3.46 r_work: 0.3236 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12263 Z= 0.184 Angle : 0.662 13.901 16647 Z= 0.335 Chirality : 0.046 0.166 1852 Planarity : 0.004 0.051 2106 Dihedral : 8.552 139.324 1724 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.56 % Allowed : 11.38 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.21), residues: 1480 helix: -0.79 (0.21), residues: 585 sheet: -2.14 (0.38), residues: 172 loop : -2.04 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 986 HIS 0.004 0.001 HIS B 347 PHE 0.016 0.002 PHE A1341 TYR 0.024 0.002 TYR A1219 ARG 0.003 0.000 ARG A 809 Details of bonding type rmsd link_NAG-ASN : bond 0.01638 ( 1) link_NAG-ASN : angle 5.76147 ( 3) link_BETA1-4 : bond 0.00378 ( 2) link_BETA1-4 : angle 3.61007 ( 6) hydrogen bonds : bond 0.03789 ( 409) hydrogen bonds : angle 5.28347 ( 1125) SS BOND : bond 0.00317 ( 2) SS BOND : angle 0.83660 ( 4) covalent geometry : bond 0.00426 (12258) covalent geometry : angle 0.65431 (16634) *********************** 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 150 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 104 time to evaluate : 1.379 Fit side-chains REVERT: A 223 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.8184 (t80) REVERT: A 224 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8417 (tm) REVERT: A 506 LEU cc_start: 0.1478 (OUTLIER) cc_final: 0.1127 (mt) REVERT: A 519 MET cc_start: 0.3599 (mtt) cc_final: 0.2427 (mmt) REVERT: A 532 MET cc_start: 0.1777 (mtt) cc_final: 0.0305 (mmt) REVERT: A 561 PHE cc_start: 0.7914 (m-80) cc_final: 0.6799 (t80) REVERT: A 691 ARG cc_start: 0.6519 (ttp-170) cc_final: 0.6058 (tpp-160) REVERT: A 847 LYS cc_start: 0.6291 (mttt) cc_final: 0.5385 (mttm) REVERT: A 964 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6987 (tt0) REVERT: A 1006 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7641 (pp) REVERT: A 1059 LYS cc_start: 0.6963 (ptpp) cc_final: 0.6660 (ptmt) REVERT: A 1196 MET cc_start: 0.8645 (tpp) cc_final: 0.8249 (mmm) REVERT: A 1212 ASP cc_start: 0.8760 (OUTLIER) cc_final: 0.8368 (t70) REVERT: B 359 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8702 (pt) REVERT: B 395 PHE cc_start: 0.7684 (m-80) cc_final: 0.7207 (m-10) outliers start: 46 outliers final: 29 residues processed: 146 average time/residue: 0.2330 time to fit residues: 51.7163 Evaluate side-chains 136 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 446 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 506 LEU 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 811 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 966 ARG 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 1095 LYS Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1122 ASP 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 A residue 1353 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 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 147 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 5 optimal weight: 0.0060 chunk 112 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.191518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.140098 restraints weight = 14506.701| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.53 r_work: 0.3277 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12263 Z= 0.150 Angle : 0.640 12.646 16647 Z= 0.321 Chirality : 0.045 0.160 1852 Planarity : 0.003 0.041 2106 Dihedral : 8.375 138.438 1724 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.79 % Allowed : 12.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.21), residues: 1480 helix: -0.67 (0.21), residues: 591 sheet: -2.01 (0.39), residues: 173 loop : -1.97 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 986 HIS 0.004 0.001 HIS B 347 PHE 0.014 0.002 PHE A1341 TYR 0.022 0.002 TYR B 280 ARG 0.003 0.000 ARG A 809 Details of bonding type rmsd link_NAG-ASN : bond 0.01321 ( 1) link_NAG-ASN : angle 5.67255 ( 3) link_BETA1-4 : bond 0.00326 ( 2) link_BETA1-4 : angle 3.43063 ( 6) hydrogen bonds : bond 0.03643 ( 409) hydrogen bonds : angle 5.20045 ( 1125) SS BOND : bond 0.00271 ( 2) SS BOND : angle 0.75197 ( 4) covalent geometry : bond 0.00345 (12258) covalent geometry : angle 0.63236 (16634) *********************** 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 147 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 1.362 Fit side-chains REVERT: A 223 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.8162 (t80) REVERT: A 224 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8448 (tm) REVERT: A 506 LEU cc_start: 0.1652 (OUTLIER) cc_final: 0.1177 (mt) REVERT: A 519 MET cc_start: 0.3544 (mtt) cc_final: 0.2431 (mmt) REVERT: A 532 MET cc_start: 0.1988 (mtt) cc_final: 0.0372 (mmt) REVERT: A 561 PHE cc_start: 0.7961 (m-80) cc_final: 0.6776 (t80) REVERT: A 691 ARG cc_start: 0.6561 (ttp-170) cc_final: 0.6153 (tpp-160) REVERT: A 847 LYS cc_start: 0.6259 (mttt) cc_final: 0.5336 (mttt) REVERT: A 964 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7195 (tt0) REVERT: A 1006 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7865 (pp) REVERT: A 1059 LYS cc_start: 0.6831 (ptpp) cc_final: 0.6527 (ptmt) REVERT: A 1115 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7287 (ttmm) REVERT: A 1196 MET cc_start: 0.8733 (tpp) cc_final: 0.8435 (mmm) REVERT: A 1212 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8415 (t70) REVERT: A 1219 TYR cc_start: 0.8458 (t80) cc_final: 0.7850 (t80) REVERT: B 80 LEU cc_start: 0.7441 (tt) cc_final: 0.7081 (tp) REVERT: B 359 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8757 (pt) REVERT: B 395 PHE cc_start: 0.7762 (m-80) cc_final: 0.7280 (m-10) outliers start: 36 outliers final: 23 residues processed: 142 average time/residue: 0.2519 time to fit residues: 52.4766 Evaluate side-chains 131 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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 506 LEU 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 964 GLU 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 1095 LYS Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1132 SER 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 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 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 11 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 87 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 115 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** B 366 HIS ** 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 = 0.4222 r_free = 0.4222 target = 0.191484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.139393 restraints weight = 14611.229| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 3.50 r_work: 0.3269 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12263 Z= 0.152 Angle : 0.640 12.602 16647 Z= 0.322 Chirality : 0.045 0.160 1852 Planarity : 0.003 0.038 2106 Dihedral : 8.273 135.448 1724 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.63 % Allowed : 13.62 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.21), residues: 1480 helix: -0.61 (0.21), residues: 595 sheet: -1.91 (0.40), residues: 171 loop : -1.96 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 986 HIS 0.003 0.001 HIS A1330 PHE 0.018 0.002 PHE A 679 TYR 0.022 0.002 TYR A 903 ARG 0.006 0.000 ARG A 264 Details of bonding type rmsd link_NAG-ASN : bond 0.01290 ( 1) link_NAG-ASN : angle 5.57328 ( 3) link_BETA1-4 : bond 0.00437 ( 2) link_BETA1-4 : angle 3.44499 ( 6) hydrogen bonds : bond 0.03605 ( 409) hydrogen bonds : angle 5.16704 ( 1125) SS BOND : bond 0.00254 ( 2) SS BOND : angle 0.74857 ( 4) covalent geometry : bond 0.00349 (12258) covalent geometry : angle 0.63276 (16634) *********************** 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 138 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: A 223 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.8144 (t80) REVERT: A 224 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8388 (tm) REVERT: A 506 LEU cc_start: 0.1637 (OUTLIER) cc_final: 0.1147 (mt) REVERT: A 519 MET cc_start: 0.3610 (mtt) cc_final: 0.2751 (mmt) REVERT: A 532 MET cc_start: 0.1801 (mtt) cc_final: 0.0276 (mmt) REVERT: A 561 PHE cc_start: 0.7836 (m-80) cc_final: 0.6714 (t80) REVERT: A 603 TRP cc_start: 0.8295 (m100) cc_final: 0.7997 (m100) REVERT: A 691 ARG cc_start: 0.6560 (ttp-170) cc_final: 0.5952 (tpp-160) REVERT: A 847 LYS cc_start: 0.6186 (mttt) cc_final: 0.5292 (mttt) REVERT: A 964 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7086 (tt0) REVERT: A 1006 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7689 (pp) REVERT: A 1091 LEU cc_start: 0.7960 (tp) cc_final: 0.7567 (mp) REVERT: A 1115 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7139 (ttmm) REVERT: A 1212 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8304 (t70) REVERT: B 80 LEU cc_start: 0.7587 (tt) cc_final: 0.7237 (tp) REVERT: B 359 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8709 (pt) REVERT: B 395 PHE cc_start: 0.7666 (m-80) cc_final: 0.7260 (m-10) outliers start: 34 outliers final: 23 residues processed: 134 average time/residue: 0.2412 time to fit residues: 48.7353 Evaluate side-chains 132 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 506 LEU 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 852 ILE Chi-restraints excluded: chain A residue 964 GLU 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 1095 LYS Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1132 SER 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 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 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 129 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 113 optimal weight: 0.0270 chunk 30 optimal weight: 0.5980 chunk 139 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 98 optimal weight: 0.2980 chunk 94 optimal weight: 0.1980 chunk 111 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 HIS ** 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 = 0.4243 r_free = 0.4243 target = 0.193601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.142969 restraints weight = 14487.049| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.42 r_work: 0.3301 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3361 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= 0.124 Angle : 0.618 12.969 16647 Z= 0.311 Chirality : 0.044 0.160 1852 Planarity : 0.003 0.034 2106 Dihedral : 8.135 135.406 1724 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.32 % Allowed : 14.01 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.22), residues: 1480 helix: -0.51 (0.21), residues: 599 sheet: -1.83 (0.40), residues: 170 loop : -1.88 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 986 HIS 0.003 0.001 HIS A1330 PHE 0.018 0.001 PHE A1402 TYR 0.021 0.002 TYR A 633 ARG 0.004 0.000 ARG A 264 Details of bonding type rmsd link_NAG-ASN : bond 0.00934 ( 1) link_NAG-ASN : angle 5.39268 ( 3) link_BETA1-4 : bond 0.00332 ( 2) link_BETA1-4 : angle 3.28459 ( 6) hydrogen bonds : bond 0.03422 ( 409) hydrogen bonds : angle 5.08233 ( 1125) SS BOND : bond 0.00168 ( 2) SS BOND : angle 0.65671 ( 4) covalent geometry : bond 0.00277 (12258) covalent geometry : angle 0.61098 (16634) *********************** 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 146 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: A 223 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.8080 (t80) REVERT: A 224 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8376 (tm) REVERT: A 506 LEU cc_start: 0.1663 (OUTLIER) cc_final: 0.1129 (mt) REVERT: A 519 MET cc_start: 0.3554 (mtt) cc_final: 0.2690 (mmt) REVERT: A 532 MET cc_start: 0.2130 (mtt) cc_final: 0.0468 (mmt) REVERT: A 561 PHE cc_start: 0.7607 (m-80) cc_final: 0.6703 (t80) REVERT: A 585 TYR cc_start: 0.8718 (m-80) cc_final: 0.7841 (m-80) REVERT: A 603 TRP cc_start: 0.8312 (m100) cc_final: 0.8068 (m100) REVERT: A 691 ARG cc_start: 0.6489 (ttp-170) cc_final: 0.5858 (tpp-160) REVERT: A 814 SER cc_start: 0.6332 (t) cc_final: 0.5580 (p) REVERT: A 847 LYS cc_start: 0.6066 (mttt) cc_final: 0.5204 (mttt) REVERT: A 1006 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7768 (pp) REVERT: A 1059 LYS cc_start: 0.6907 (ptpp) cc_final: 0.6562 (pttt) REVERT: A 1091 LEU cc_start: 0.7941 (tp) cc_final: 0.7546 (mp) REVERT: A 1212 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8298 (t70) REVERT: B 80 LEU cc_start: 0.7561 (tt) cc_final: 0.7203 (tp) REVERT: B 359 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8637 (pt) REVERT: B 395 PHE cc_start: 0.7653 (m-80) cc_final: 0.7287 (m-10) outliers start: 30 outliers final: 19 residues processed: 141 average time/residue: 0.2569 time to fit residues: 52.9626 Evaluate side-chains 132 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 506 LEU 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 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 1095 LYS Chi-restraints excluded: chain A residue 1212 ASP Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1353 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 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 117 optimal weight: 0.5980 chunk 137 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 100 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.191848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.139601 restraints weight = 14489.117| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 3.34 r_work: 0.3279 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 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 0.057 12263 Z= 0.155 Angle : 0.637 10.368 16647 Z= 0.320 Chirality : 0.045 0.161 1852 Planarity : 0.004 0.044 2106 Dihedral : 8.169 135.379 1724 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.32 % Allowed : 14.01 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.22), residues: 1480 helix: -0.49 (0.21), residues: 600 sheet: -1.73 (0.41), residues: 170 loop : -1.84 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 986 HIS 0.003 0.001 HIS A1330 PHE 0.015 0.002 PHE A1224 TYR 0.021 0.002 TYR B 280 ARG 0.005 0.000 ARG A1262 Details of bonding type rmsd link_NAG-ASN : bond 0.01223 ( 1) link_NAG-ASN : angle 5.46932 ( 3) link_BETA1-4 : bond 0.00390 ( 2) link_BETA1-4 : angle 3.46941 ( 6) hydrogen bonds : bond 0.03565 ( 409) hydrogen bonds : angle 5.09925 ( 1125) SS BOND : bond 0.00263 ( 2) SS BOND : angle 0.75033 ( 4) covalent geometry : bond 0.00358 (12258) covalent geometry : angle 0.62985 (16634) ********************** 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 134 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: A 223 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.8036 (t80) REVERT: A 224 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8392 (tm) REVERT: A 506 LEU cc_start: 0.1647 (OUTLIER) cc_final: 0.1099 (mt) REVERT: A 519 MET cc_start: 0.3560 (mtt) cc_final: 0.2697 (mmt) REVERT: A 532 MET cc_start: 0.2111 (mtt) cc_final: 0.0460 (mmt) REVERT: A 561 PHE cc_start: 0.7671 (m-80) cc_final: 0.6744 (t80) REVERT: A 603 TRP cc_start: 0.8314 (m100) cc_final: 0.8056 (m100) REVERT: A 691 ARG cc_start: 0.6506 (ttp-170) cc_final: 0.5805 (tpp-160) REVERT: A 795 LYS cc_start: 0.7174 (mmtm) cc_final: 0.6875 (mmtm) REVERT: A 847 LYS cc_start: 0.6178 (mttt) cc_final: 0.5270 (mttt) REVERT: A 1006 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7751 (pp) REVERT: A 1009 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7269 (pm20) REVERT: A 1059 LYS cc_start: 0.7066 (ptpp) cc_final: 0.6746 (ptmt) REVERT: A 1115 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7162 (ttmm) REVERT: A 1196 MET cc_start: 0.8558 (tpp) cc_final: 0.8016 (mmm) REVERT: A 1212 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8298 (t70) REVERT: A 1274 MET cc_start: 0.8399 (mmm) cc_final: 0.8166 (mmm) REVERT: B 80 LEU cc_start: 0.7597 (tt) cc_final: 0.7231 (tp) REVERT: B 395 PHE cc_start: 0.7735 (m-80) cc_final: 0.7402 (m-10) outliers start: 30 outliers final: 19 residues processed: 131 average time/residue: 0.2543 time to fit residues: 50.6199 Evaluate side-chains 129 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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 506 LEU 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 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 1009 GLU Chi-restraints excluded: chain A residue 1095 LYS Chi-restraints excluded: chain A residue 1115 LYS Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1212 ASP Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1353 THR 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 409 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 93 optimal weight: 0.0980 chunk 133 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 112 optimal weight: 0.0010 chunk 124 optimal weight: 0.8980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 ASN ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1004 ASN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4233 r_free = 0.4233 target = 0.192695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.141134 restraints weight = 14340.994| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.23 r_work: 0.3272 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3511 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= 0.153 Angle : 0.628 7.921 16647 Z= 0.318 Chirality : 0.045 0.159 1852 Planarity : 0.003 0.036 2106 Dihedral : 8.140 134.577 1724 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.24 % Allowed : 14.40 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.22), residues: 1480 helix: -0.46 (0.21), residues: 602 sheet: -1.59 (0.43), residues: 160 loop : -1.87 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 986 HIS 0.004 0.001 HIS A1330 PHE 0.029 0.002 PHE A1402 TYR 0.021 0.002 TYR B 280 ARG 0.004 0.000 ARG A 264 Details of bonding type rmsd link_NAG-ASN : bond 0.01145 ( 1) link_NAG-ASN : angle 5.36125 ( 3) link_BETA1-4 : bond 0.00380 ( 2) link_BETA1-4 : angle 3.49150 ( 6) hydrogen bonds : bond 0.03584 ( 409) hydrogen bonds : angle 5.05423 ( 1125) SS BOND : bond 0.00270 ( 2) SS BOND : angle 0.76854 ( 4) covalent geometry : bond 0.00353 (12258) covalent geometry : angle 0.62071 (16634) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7828.71 seconds wall clock time: 137 minutes 44.38 seconds (8264.38 seconds total)