Starting phenix.real_space_refine on Thu Jul 31 06:54:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pzk_20536/07_2025/6pzk_20536.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pzk_20536/07_2025/6pzk_20536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pzk_20536/07_2025/6pzk_20536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pzk_20536/07_2025/6pzk_20536.map" model { file = "/net/cci-nas-00/data/ceres_data/6pzk_20536/07_2025/6pzk_20536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pzk_20536/07_2025/6pzk_20536.cif" } resolution = 3.2 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= 0.088 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: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 8407 2.51 5 N 2237 2.21 5 O 2436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13153 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1361, 11106 Classifications: {'peptide': 1361} Link IDs: {'PTRANS': 47, 'TRANS': 1313} Chain breaks: 3 Chain: "B" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 762 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "C" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 437 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "D" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "E" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'TRANS': 52} Chain breaks: 1 Time building chain proxies: 8.70, per 1000 atoms: 0.66 Number of scatterers: 13153 At special positions: 0 Unit cell: (97.825, 119.325, 117.175, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 73 16.00 O 2436 8.00 N 2237 7.00 C 8407 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.44 Conformation dependent library (CDL) restraints added in 3.7 seconds 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3116 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 8 sheets defined 65.1% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 55 through 63 removed outlier: 4.148A pdb=" N LEU A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 83 through 93 removed outlier: 4.060A pdb=" N PHE A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 131 removed outlier: 4.732A pdb=" N VAL A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 Processing helix chain 'A' and resid 201 through 228 removed outlier: 3.743A pdb=" N TRP A 207 " --> pdb=" O TRP A 203 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 296 removed outlier: 3.701A pdb=" N PHE A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 325 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 334 through 348 removed outlier: 3.601A pdb=" N ILE A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 379 removed outlier: 3.917A pdb=" N ARG A 355 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.626A pdb=" N ILE A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.704A pdb=" N LEU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 422 Processing helix chain 'A' and resid 423 through 427 Processing helix chain 'A' and resid 437 through 449 removed outlier: 4.052A pdb=" N VAL A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE A 445 " --> pdb=" O ASP A 441 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASN A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 449 " --> pdb=" O ILE A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 478 removed outlier: 3.501A pdb=" N ASN A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 490 through 499 removed outlier: 4.363A pdb=" N TYR A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 545 through 553 removed outlier: 5.255A pdb=" N TRP A 550 " --> pdb=" O ASN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 559 through 570 removed outlier: 3.967A pdb=" N TYR A 565 " --> pdb=" O HIS A 561 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N HIS A 568 " --> pdb=" O ASN A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 576 through 580 removed outlier: 4.336A pdb=" N ARG A 580 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 593 through 596 Processing helix chain 'A' and resid 597 through 602 Processing helix chain 'A' and resid 633 through 651 removed outlier: 3.647A pdb=" N VAL A 639 " --> pdb=" O MET A 635 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 655 Processing helix chain 'A' and resid 703 through 708 removed outlier: 3.644A pdb=" N ALA A 707 " --> pdb=" O LYS A 703 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE A 708 " --> pdb=" O PHE A 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 703 through 708' Processing helix chain 'A' and resid 709 through 712 Processing helix chain 'A' and resid 713 through 724 removed outlier: 3.760A pdb=" N VAL A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 737 Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 781 through 800 removed outlier: 4.183A pdb=" N LEU A 798 " --> pdb=" O ASP A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 850 Processing helix chain 'A' and resid 868 through 872 removed outlier: 4.214A pdb=" N LYS A 871 " --> pdb=" O PHE A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 888 removed outlier: 3.933A pdb=" N LYS A 886 " --> pdb=" O ALA A 882 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 887 " --> pdb=" O SER A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 913 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 921 through 939 Processing helix chain 'A' and resid 940 through 944 removed outlier: 3.719A pdb=" N HIS A 944 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 966 Processing helix chain 'A' and resid 970 through 979 Processing helix chain 'A' and resid 982 through 986 Processing helix chain 'A' and resid 1003 through 1021 removed outlier: 4.226A pdb=" N GLU A1007 " --> pdb=" O ASP A1003 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1045 Processing helix chain 'A' and resid 1054 through 1060 Processing helix chain 'A' and resid 1072 through 1086 removed outlier: 5.027A pdb=" N LEU A1079 " --> pdb=" O GLU A1075 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ALA A1080 " --> pdb=" O ILE A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1110 removed outlier: 4.346A pdb=" N SER A1096 " --> pdb=" O ILE A1092 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N THR A1101 " --> pdb=" O ALA A1097 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N THR A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A1108 " --> pdb=" O GLU A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1129 Processing helix chain 'A' and resid 1130 through 1142 removed outlier: 3.732A pdb=" N ILE A1137 " --> pdb=" O LYS A1133 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A1138 " --> pdb=" O ALA A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1153 removed outlier: 5.734A pdb=" N LEU A1151 " --> pdb=" O THR A1148 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A1153 " --> pdb=" O ILE A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1180 removed outlier: 5.299A pdb=" N LEU A1176 " --> pdb=" O ASN A1172 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE A1177 " --> pdb=" O ILE A1173 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A1178 " --> pdb=" O THR A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1188 Processing helix chain 'A' and resid 1198 through 1210 Processing helix chain 'A' and resid 1223 through 1227 Processing helix chain 'A' and resid 1277 through 1281 removed outlier: 3.529A pdb=" N LEU A1281 " --> pdb=" O ARG A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1299 removed outlier: 4.638A pdb=" N GLN A1288 " --> pdb=" O LYS A1284 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP A1290 " --> pdb=" O ARG A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1302 No H-bonds generated for 'chain 'A' and resid 1300 through 1302' Processing helix chain 'A' and resid 1304 through 1316 Processing helix chain 'A' and resid 1320 through 1325 Processing helix chain 'A' and resid 1326 through 1328 No H-bonds generated for 'chain 'A' and resid 1326 through 1328' Processing helix chain 'A' and resid 1354 through 1359 Processing helix chain 'A' and resid 1365 through 1375 removed outlier: 3.822A pdb=" N ARG A1370 " --> pdb=" O SER A1366 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE A1371 " --> pdb=" O PRO A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1404 removed outlier: 3.532A pdb=" N SER A1397 " --> pdb=" O LEU A1393 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU A1400 " --> pdb=" O MET A1396 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1419 Processing helix chain 'A' and resid 1432 through 1443 Processing helix chain 'A' and resid 1444 through 1447 Processing helix chain 'A' and resid 1452 through 1460 removed outlier: 4.509A pdb=" N GLU A1458 " --> pdb=" O THR A1454 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 150 removed outlier: 4.610A pdb=" N ARG B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B 141 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 164 removed outlier: 4.000A pdb=" N ASP B 164 " --> pdb=" O SER B 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 161 through 164' Processing helix chain 'B' and resid 174 through 183 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 203 through 210 Processing helix chain 'B' and resid 217 through 228 removed outlier: 4.535A pdb=" N ASN B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU B 226 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 157 removed outlier: 3.507A pdb=" N ARG C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS C 141 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 144 " --> pdb=" O GLU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 164 Processing helix chain 'C' and resid 167 through 172 Processing helix chain 'C' and resid 174 through 185 Processing helix chain 'D' and resid 131 through 156 removed outlier: 4.803A pdb=" N ASP D 136 " --> pdb=" O THR D 132 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 154 " --> pdb=" O HIS D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 182 removed outlier: 4.011A pdb=" N ILE D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG D 167 " --> pdb=" O ARG D 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 155 removed outlier: 3.635A pdb=" N GLY E 147 " --> pdb=" O SER E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 199 removed outlier: 3.762A pdb=" N LEU E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG E 191 " --> pdb=" O MET E 187 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU E 192 " --> pdb=" O THR E 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.415A pdb=" N LYS A 80 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N VAL A 263 " --> pdb=" O LYS A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 629 through 631 Processing sheet with id=AA4, first strand: chain 'A' and resid 803 through 809 Processing sheet with id=AA5, first strand: chain 'A' and resid 873 through 875 removed outlier: 3.668A pdb=" N ILE A 873 " --> pdb=" O TYR A 880 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1228 through 1231 Processing sheet with id=AA7, first strand: chain 'A' and resid 1271 through 1272 Processing sheet with id=AA8, first strand: chain 'B' and resid 158 through 159 716 hydrogen bonds defined for protein. 2025 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: 5.46 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2599 1.32 - 1.45: 2997 1.45 - 1.57: 7671 1.57 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 13390 Sorted by residual: bond pdb=" CZ ARG A1357 " pdb=" NH2 ARG A1357 " ideal model delta sigma weight residual 1.330 1.280 0.050 1.30e-02 5.92e+03 1.47e+01 bond pdb=" CZ ARG A 302 " pdb=" NH2 ARG A 302 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.30e-02 5.92e+03 1.37e+01 bond pdb=" CZ ARG C 167 " pdb=" NH2 ARG C 167 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.30e-02 5.92e+03 1.36e+01 bond pdb=" CZ ARG A 279 " pdb=" NH2 ARG A 279 " ideal model delta sigma weight residual 1.330 1.284 0.046 1.30e-02 5.92e+03 1.26e+01 bond pdb=" CZ ARG A1123 " pdb=" NH2 ARG A1123 " ideal model delta sigma weight residual 1.330 1.284 0.046 1.30e-02 5.92e+03 1.24e+01 ... (remaining 13385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 13793 2.25 - 4.51: 3897 4.51 - 6.76: 380 6.76 - 9.01: 19 9.01 - 11.26: 6 Bond angle restraints: 18095 Sorted by residual: angle pdb=" CA HIS A1444 " pdb=" CB HIS A1444 " pdb=" CG HIS A1444 " ideal model delta sigma weight residual 113.80 122.80 -9.00 1.00e+00 1.00e+00 8.10e+01 angle pdb=" N MET A 869 " pdb=" CA MET A 869 " pdb=" C MET A 869 " ideal model delta sigma weight residual 110.23 121.49 -11.26 1.45e+00 4.76e-01 6.03e+01 angle pdb=" C PHE A 521 " pdb=" N TYR A 522 " pdb=" CA TYR A 522 " ideal model delta sigma weight residual 122.59 133.47 -10.88 1.57e+00 4.06e-01 4.80e+01 angle pdb=" C HIS A1444 " pdb=" CA HIS A1444 " pdb=" CB HIS A1444 " ideal model delta sigma weight residual 110.74 99.49 11.25 1.66e+00 3.63e-01 4.59e+01 angle pdb=" CA ASP A 700 " pdb=" CB ASP A 700 " pdb=" CG ASP A 700 " ideal model delta sigma weight residual 112.60 119.30 -6.70 1.00e+00 1.00e+00 4.49e+01 ... (remaining 18090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7436 17.90 - 35.80: 605 35.80 - 53.71: 98 53.71 - 71.61: 35 71.61 - 89.51: 14 Dihedral angle restraints: 8188 sinusoidal: 3389 harmonic: 4799 Sorted by residual: dihedral pdb=" C MET A 869 " pdb=" N MET A 869 " pdb=" CA MET A 869 " pdb=" CB MET A 869 " ideal model delta harmonic sigma weight residual -122.60 -151.88 29.28 0 2.50e+00 1.60e-01 1.37e+02 dihedral pdb=" N MET A 869 " pdb=" C MET A 869 " pdb=" CA MET A 869 " pdb=" CB MET A 869 " ideal model delta harmonic sigma weight residual 122.80 151.24 -28.44 0 2.50e+00 1.60e-01 1.29e+02 dihedral pdb=" C ARG B 182 " pdb=" N ARG B 182 " pdb=" CA ARG B 182 " pdb=" CB ARG B 182 " ideal model delta harmonic sigma weight residual -122.60 -150.85 28.25 0 2.50e+00 1.60e-01 1.28e+02 ... (remaining 8185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.250: 2038 0.250 - 0.499: 53 0.499 - 0.749: 2 0.749 - 0.998: 2 0.998 - 1.248: 2 Chirality restraints: 2097 Sorted by residual: chirality pdb=" CA MET A 869 " pdb=" N MET A 869 " pdb=" C MET A 869 " pdb=" CB MET A 869 " both_signs ideal model delta sigma weight residual False 2.51 1.26 1.25 2.00e-01 2.50e+01 3.89e+01 chirality pdb=" CA ARG B 182 " pdb=" N ARG B 182 " pdb=" C ARG B 182 " pdb=" CB ARG B 182 " both_signs ideal model delta sigma weight residual False 2.51 1.36 1.15 2.00e-01 2.50e+01 3.28e+01 chirality pdb=" CA GLU A1374 " pdb=" N GLU A1374 " pdb=" C GLU A1374 " pdb=" CB GLU A1374 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.84e+01 ... (remaining 2094 not shown) Planarity restraints: 2271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 586 " -0.173 2.00e-02 2.50e+03 9.34e-02 1.75e+02 pdb=" CG TYR A 586 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR A 586 " 0.076 2.00e-02 2.50e+03 pdb=" CD2 TYR A 586 " 0.079 2.00e-02 2.50e+03 pdb=" CE1 TYR A 586 " 0.053 2.00e-02 2.50e+03 pdb=" CE2 TYR A 586 " 0.050 2.00e-02 2.50e+03 pdb=" CZ TYR A 586 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 586 " -0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 770 " -0.164 2.00e-02 2.50e+03 9.14e-02 1.67e+02 pdb=" CG TYR A 770 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 770 " 0.073 2.00e-02 2.50e+03 pdb=" CD2 TYR A 770 " 0.069 2.00e-02 2.50e+03 pdb=" CE1 TYR A 770 " 0.058 2.00e-02 2.50e+03 pdb=" CE2 TYR A 770 " 0.054 2.00e-02 2.50e+03 pdb=" CZ TYR A 770 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 770 " -0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 834 " -0.141 2.00e-02 2.50e+03 7.96e-02 1.27e+02 pdb=" CG TYR A 834 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 834 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 TYR A 834 " 0.068 2.00e-02 2.50e+03 pdb=" CE1 TYR A 834 " 0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR A 834 " 0.049 2.00e-02 2.50e+03 pdb=" CZ TYR A 834 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 834 " -0.128 2.00e-02 2.50e+03 ... (remaining 2268 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 6445 3.01 - 3.48: 14108 3.48 - 3.95: 21757 3.95 - 4.43: 24915 4.43 - 4.90: 41097 Nonbonded interactions: 108322 Sorted by model distance: nonbonded pdb=" OD1 ASP A1296 " pdb=" OH TYR A1321 " model vdw 2.533 3.040 nonbonded pdb=" OD2 ASP A1003 " pdb=" OG1 THR A1006 " model vdw 2.533 3.040 nonbonded pdb=" OH TYR A1100 " pdb=" OE1 GLU A1135 " model vdw 2.533 3.040 nonbonded pdb=" N TYR A 522 " pdb=" O TYR A 522 " model vdw 2.552 2.496 nonbonded pdb=" OE1 GLU A 27 " pdb=" OG1 THR A 265 " model vdw 2.554 3.040 ... (remaining 108317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and resid 130 through 184) selection = chain 'D' } 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: 42.910 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: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 37.300 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 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 : 0.012 0.061 13390 Z= 0.744 Angle : 1.931 11.263 18095 Z= 1.298 Chirality : 0.117 1.248 2097 Planarity : 0.016 0.142 2271 Dihedral : 14.419 89.507 5072 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 0.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.95 % Allowed : 5.91 % Favored : 92.14 % Cbeta Deviations : 1.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.86 (0.18), residues: 1606 helix: -2.53 (0.12), residues: 925 sheet: 0.53 (0.60), residues: 67 loop : -0.77 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.098 0.024 TRP A 732 HIS 0.020 0.004 HIS A1011 PHE 0.128 0.016 PHE A 269 TYR 0.173 0.025 TYR A 586 ARG 0.019 0.002 ARG A1059 Details of bonding type rmsd hydrogen bonds : bond 0.19721 ( 716) hydrogen bonds : angle 8.11481 ( 2025) covalent geometry : bond 0.01198 (13390) covalent geometry : angle 1.93051 (18095) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 366 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 SER cc_start: 0.8375 (t) cc_final: 0.8137 (m) REVERT: A 471 LYS cc_start: 0.7755 (tttt) cc_final: 0.7450 (tttp) REVERT: A 644 GLU cc_start: 0.7475 (tp30) cc_final: 0.6992 (mm-30) REVERT: A 645 LYS cc_start: 0.8113 (tptm) cc_final: 0.7896 (tptt) REVERT: A 694 LYS cc_start: 0.7875 (ttmt) cc_final: 0.7178 (ttpp) REVERT: A 727 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7250 (mt0) REVERT: A 794 ASP cc_start: 0.7910 (m-30) cc_final: 0.7651 (m-30) REVERT: A 801 LYS cc_start: 0.8173 (pttt) cc_final: 0.7896 (mmtm) REVERT: A 807 LEU cc_start: 0.8035 (tp) cc_final: 0.7422 (mt) REVERT: A 979 MET cc_start: 0.8535 (mmm) cc_final: 0.8237 (tpp) REVERT: A 1075 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7660 (tm-30) REVERT: A 1078 ARG cc_start: 0.7738 (ptp-110) cc_final: 0.7377 (mtm110) REVERT: A 1112 GLN cc_start: 0.7730 (tt0) cc_final: 0.7175 (pt0) REVERT: A 1164 ARG cc_start: 0.8039 (ttm110) cc_final: 0.7816 (ttp80) REVERT: A 1260 LYS cc_start: 0.8249 (ptmm) cc_final: 0.8026 (tttp) REVERT: A 1304 ASN cc_start: 0.7152 (t0) cc_final: 0.6836 (t0) REVERT: C 148 MET cc_start: 0.7895 (mmm) cc_final: 0.7573 (mmt) REVERT: C 164 ASP cc_start: 0.7659 (m-30) cc_final: 0.7257 (m-30) REVERT: D 150 HIS cc_start: 0.7779 (m-70) cc_final: 0.7155 (m90) outliers start: 29 outliers final: 6 residues processed: 386 average time/residue: 0.3067 time to fit residues: 167.0387 Evaluate side-chains 244 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 237 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 600 CYS Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 52 GLN A 229 HIS A 248 GLN A 296 ASN A 306 ASN A 325 HIS A 362 ASN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN A 773 HIS A 853 HIS A 970 ASN ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN A1438 GLN B 224 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.160211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.127307 restraints weight = 14530.309| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.20 r_work: 0.3349 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13390 Z= 0.164 Angle : 0.667 10.378 18095 Z= 0.353 Chirality : 0.045 0.168 2097 Planarity : 0.004 0.041 2271 Dihedral : 6.254 48.008 1782 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.28 % Allowed : 12.22 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.32 (0.20), residues: 1606 helix: -0.30 (0.16), residues: 926 sheet: 1.07 (0.60), residues: 70 loop : 0.07 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 932 HIS 0.011 0.001 HIS A1444 PHE 0.021 0.002 PHE A 704 TYR 0.024 0.002 TYR A1018 ARG 0.005 0.001 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.04481 ( 716) hydrogen bonds : angle 4.68817 ( 2025) covalent geometry : bond 0.00376 (13390) covalent geometry : angle 0.66662 (18095) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8231 (tttt) cc_final: 0.7994 (ttpp) REVERT: A 240 SER cc_start: 0.8329 (t) cc_final: 0.8113 (m) REVERT: A 389 SER cc_start: 0.8482 (m) cc_final: 0.8249 (p) REVERT: A 409 LYS cc_start: 0.7326 (tttt) cc_final: 0.6877 (ttmm) REVERT: A 498 LYS cc_start: 0.8417 (mtpt) cc_final: 0.7787 (mmmt) REVERT: A 511 ARG cc_start: 0.7022 (tpp80) cc_final: 0.6062 (tpp80) REVERT: A 594 GLU cc_start: 0.8209 (mp0) cc_final: 0.7061 (mm-30) REVERT: A 595 CYS cc_start: 0.7115 (m) cc_final: 0.6909 (p) REVERT: A 645 LYS cc_start: 0.8010 (tptm) cc_final: 0.7805 (tptt) REVERT: A 694 LYS cc_start: 0.8119 (ttmt) cc_final: 0.7060 (ttpt) REVERT: A 705 ASN cc_start: 0.8595 (p0) cc_final: 0.8002 (m-40) REVERT: A 736 THR cc_start: 0.8522 (p) cc_final: 0.8218 (t) REVERT: A 801 LYS cc_start: 0.8092 (pttt) cc_final: 0.7453 (mmtm) REVERT: A 807 LEU cc_start: 0.7806 (tp) cc_final: 0.7177 (mt) REVERT: A 979 MET cc_start: 0.8660 (mmm) cc_final: 0.8214 (tpp) REVERT: A 1091 LYS cc_start: 0.7894 (mmmm) cc_final: 0.7666 (tppp) REVERT: A 1112 GLN cc_start: 0.8092 (tt0) cc_final: 0.7030 (pt0) REVERT: A 1135 GLU cc_start: 0.7946 (tp30) cc_final: 0.7712 (tp30) REVERT: A 1217 VAL cc_start: 0.8254 (t) cc_final: 0.8001 (m) REVERT: A 1246 TYR cc_start: 0.7188 (m-10) cc_final: 0.6621 (m-10) REVERT: A 1255 GLU cc_start: 0.7495 (tt0) cc_final: 0.7042 (mt-10) REVERT: A 1270 LYS cc_start: 0.6296 (OUTLIER) cc_final: 0.5917 (ttmt) REVERT: A 1284 LYS cc_start: 0.8432 (ptmt) cc_final: 0.8158 (ptmt) REVERT: A 1323 LYS cc_start: 0.7680 (mmtt) cc_final: 0.7443 (mtpt) REVERT: A 1376 TYR cc_start: 0.8334 (m-80) cc_final: 0.8067 (m-10) REVERT: B 187 MET cc_start: 0.5818 (mmm) cc_final: 0.3020 (ptp) REVERT: C 164 ASP cc_start: 0.7788 (m-30) cc_final: 0.7291 (m-30) outliers start: 34 outliers final: 19 residues processed: 269 average time/residue: 0.2898 time to fit residues: 110.4164 Evaluate side-chains 223 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1191 ILE Chi-restraints excluded: chain A residue 1194 MET Chi-restraints excluded: chain A residue 1270 LYS Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 173 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 37 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 141 optimal weight: 0.0970 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 255 HIS ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 HIS A 748 HIS ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1444 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.159563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.126279 restraints weight = 14611.978| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.24 r_work: 0.3356 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13390 Z= 0.138 Angle : 0.578 10.350 18095 Z= 0.303 Chirality : 0.042 0.213 2097 Planarity : 0.004 0.044 2271 Dihedral : 5.310 39.531 1775 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.82 % Allowed : 13.30 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.47 (0.21), residues: 1606 helix: 0.47 (0.17), residues: 929 sheet: 1.03 (0.60), residues: 70 loop : 0.21 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 932 HIS 0.013 0.001 HIS A1444 PHE 0.017 0.002 PHE A 87 TYR 0.019 0.002 TYR A 746 ARG 0.007 0.000 ARG A 511 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 716) hydrogen bonds : angle 4.31784 ( 2025) covalent geometry : bond 0.00316 (13390) covalent geometry : angle 0.57760 (18095) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 218 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 ASN cc_start: 0.7679 (t0) cc_final: 0.7427 (m-40) REVERT: A 389 SER cc_start: 0.8492 (m) cc_final: 0.8169 (p) REVERT: A 409 LYS cc_start: 0.7414 (tttt) cc_final: 0.6972 (ttmm) REVERT: A 498 LYS cc_start: 0.8377 (mtpt) cc_final: 0.7780 (mmmt) REVERT: A 511 ARG cc_start: 0.6843 (tpp80) cc_final: 0.6343 (tpp80) REVERT: A 594 GLU cc_start: 0.8222 (mp0) cc_final: 0.6979 (mm-30) REVERT: A 595 CYS cc_start: 0.7181 (m) cc_final: 0.6895 (p) REVERT: A 645 LYS cc_start: 0.7981 (tptm) cc_final: 0.7759 (tptt) REVERT: A 694 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7133 (ttpp) REVERT: A 705 ASN cc_start: 0.8671 (p0) cc_final: 0.8042 (m-40) REVERT: A 727 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7118 (mt0) REVERT: A 736 THR cc_start: 0.8627 (p) cc_final: 0.8351 (t) REVERT: A 774 MET cc_start: 0.8519 (mmm) cc_final: 0.8052 (mmt) REVERT: A 807 LEU cc_start: 0.7901 (tp) cc_final: 0.7299 (mt) REVERT: A 824 MET cc_start: 0.6819 (pmm) cc_final: 0.6381 (pmm) REVERT: A 874 GLN cc_start: 0.8098 (mt0) cc_final: 0.7515 (tt0) REVERT: A 979 MET cc_start: 0.8652 (mmm) cc_final: 0.8256 (tpp) REVERT: A 1091 LYS cc_start: 0.7788 (mmmm) cc_final: 0.7477 (tppp) REVERT: A 1112 GLN cc_start: 0.8033 (tt0) cc_final: 0.6810 (pt0) REVERT: A 1135 GLU cc_start: 0.7769 (tp30) cc_final: 0.7413 (tp30) REVERT: A 1217 VAL cc_start: 0.8283 (t) cc_final: 0.8059 (m) REVERT: A 1246 TYR cc_start: 0.7215 (m-10) cc_final: 0.6783 (m-10) REVERT: A 1255 GLU cc_start: 0.7562 (tt0) cc_final: 0.7067 (mt-10) REVERT: A 1348 GLU cc_start: 0.8089 (pt0) cc_final: 0.7554 (mt-10) REVERT: B 187 MET cc_start: 0.6126 (mmm) cc_final: 0.3291 (ptp) REVERT: C 164 ASP cc_start: 0.7972 (m-30) cc_final: 0.7466 (m-30) outliers start: 42 outliers final: 24 residues processed: 248 average time/residue: 0.2670 time to fit residues: 96.2264 Evaluate side-chains 218 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1191 ILE Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 219 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 6 optimal weight: 0.0370 chunk 134 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 115 optimal weight: 0.4980 chunk 101 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 248 GLN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1288 GLN A1444 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.167454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.139091 restraints weight = 14084.114| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.71 r_work: 0.3445 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13390 Z= 0.118 Angle : 0.529 9.049 18095 Z= 0.276 Chirality : 0.041 0.166 2097 Planarity : 0.003 0.044 2271 Dihedral : 4.793 38.122 1772 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.48 % Allowed : 15.51 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.93 (0.21), residues: 1606 helix: 0.89 (0.17), residues: 936 sheet: 1.00 (0.61), residues: 70 loop : 0.35 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 932 HIS 0.010 0.001 HIS A1444 PHE 0.014 0.001 PHE A 87 TYR 0.019 0.001 TYR A 86 ARG 0.005 0.000 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 716) hydrogen bonds : angle 4.08671 ( 2025) covalent geometry : bond 0.00266 (13390) covalent geometry : angle 0.52919 (18095) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASN cc_start: 0.8178 (t0) cc_final: 0.7786 (m110) REVERT: A 238 THR cc_start: 0.8901 (p) cc_final: 0.8612 (t) REVERT: A 409 LYS cc_start: 0.8066 (tttt) cc_final: 0.7691 (ttmm) REVERT: A 498 LYS cc_start: 0.8534 (mtpt) cc_final: 0.7987 (mmmt) REVERT: A 594 GLU cc_start: 0.8383 (mp0) cc_final: 0.7440 (mm-30) REVERT: A 645 LYS cc_start: 0.8437 (tptm) cc_final: 0.8177 (tptt) REVERT: A 694 LYS cc_start: 0.8448 (ttmt) cc_final: 0.7463 (ttpp) REVERT: A 705 ASN cc_start: 0.8860 (p0) cc_final: 0.8230 (m-40) REVERT: A 736 THR cc_start: 0.8866 (p) cc_final: 0.8646 (t) REVERT: A 774 MET cc_start: 0.8593 (mmm) cc_final: 0.7891 (mmt) REVERT: A 794 ASP cc_start: 0.7841 (m-30) cc_final: 0.7505 (m-30) REVERT: A 807 LEU cc_start: 0.8352 (tp) cc_final: 0.7794 (mt) REVERT: A 1091 LYS cc_start: 0.8309 (mmmm) cc_final: 0.8003 (tppp) REVERT: A 1112 GLN cc_start: 0.8140 (tt0) cc_final: 0.7308 (pt0) REVERT: A 1135 GLU cc_start: 0.8018 (tp30) cc_final: 0.7723 (mm-30) REVERT: A 1225 MET cc_start: 0.8129 (ttp) cc_final: 0.7726 (ttp) REVERT: A 1246 TYR cc_start: 0.7482 (m-10) cc_final: 0.7176 (m-10) REVERT: A 1255 GLU cc_start: 0.7549 (tt0) cc_final: 0.7263 (mt-10) REVERT: C 164 ASP cc_start: 0.8113 (m-30) cc_final: 0.7635 (m-30) outliers start: 37 outliers final: 19 residues processed: 238 average time/residue: 0.2482 time to fit residues: 87.2995 Evaluate side-chains 207 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1191 ILE Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 219 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 81 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 306 ASN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 GLN ** A 724 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN A 867 GLN A1185 ASN A1247 ASN B 225 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.162552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.131848 restraints weight = 14405.236| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.88 r_work: 0.3411 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13390 Z= 0.177 Angle : 0.579 9.848 18095 Z= 0.298 Chirality : 0.043 0.162 2097 Planarity : 0.004 0.046 2271 Dihedral : 4.790 38.227 1772 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.96 % Allowed : 15.85 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.99 (0.21), residues: 1606 helix: 0.99 (0.17), residues: 930 sheet: 0.52 (0.59), residues: 75 loop : 0.34 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 932 HIS 0.005 0.001 HIS C 150 PHE 0.015 0.002 PHE A 424 TYR 0.016 0.002 TYR A 746 ARG 0.007 0.000 ARG E 134 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 716) hydrogen bonds : angle 4.16811 ( 2025) covalent geometry : bond 0.00431 (13390) covalent geometry : angle 0.57864 (18095) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 1.436 Fit side-chains revert: symmetry clash REVERT: A 23 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.7984 (mt) REVERT: A 53 ASN cc_start: 0.8359 (t0) cc_final: 0.7932 (m110) REVERT: A 238 THR cc_start: 0.8969 (p) cc_final: 0.8743 (t) REVERT: A 409 LYS cc_start: 0.8119 (tttt) cc_final: 0.7915 (ttmt) REVERT: A 498 LYS cc_start: 0.8565 (mtpt) cc_final: 0.8043 (mmmt) REVERT: A 542 ILE cc_start: 0.7961 (tt) cc_final: 0.7685 (tt) REVERT: A 594 GLU cc_start: 0.8404 (mp0) cc_final: 0.7355 (mt-10) REVERT: A 645 LYS cc_start: 0.8492 (tptm) cc_final: 0.8244 (tptt) REVERT: A 694 LYS cc_start: 0.8481 (ttmt) cc_final: 0.7570 (tmtt) REVERT: A 736 THR cc_start: 0.8962 (p) cc_final: 0.8725 (t) REVERT: A 794 ASP cc_start: 0.7935 (m-30) cc_final: 0.7624 (m-30) REVERT: A 807 LEU cc_start: 0.8264 (tp) cc_final: 0.7662 (mt) REVERT: A 1091 LYS cc_start: 0.8332 (mmmm) cc_final: 0.8027 (tppp) REVERT: A 1112 GLN cc_start: 0.8228 (tt0) cc_final: 0.7334 (pt0) REVERT: A 1133 LYS cc_start: 0.8165 (ttpt) cc_final: 0.6878 (mppt) REVERT: A 1135 GLU cc_start: 0.8092 (tp30) cc_final: 0.7804 (tp30) REVERT: A 1255 GLU cc_start: 0.7645 (tt0) cc_final: 0.7266 (mt-10) REVERT: A 1284 LYS cc_start: 0.8557 (ptmt) cc_final: 0.8320 (ptmm) REVERT: B 187 MET cc_start: 0.6639 (mmm) cc_final: 0.3665 (ptp) REVERT: E 195 MET cc_start: 0.6465 (ppp) cc_final: 0.5127 (tpp) outliers start: 44 outliers final: 31 residues processed: 230 average time/residue: 0.2400 time to fit residues: 82.3813 Evaluate side-chains 212 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 600 CYS Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1191 ILE Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1373 THR Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 219 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 147 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 114 optimal weight: 0.0570 chunk 14 optimal weight: 0.0270 chunk 142 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 296 ASN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A 724 HIS A 727 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.162287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.133282 restraints weight = 14430.934| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.76 r_work: 0.3473 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13390 Z= 0.113 Angle : 0.523 8.887 18095 Z= 0.272 Chirality : 0.040 0.141 2097 Planarity : 0.003 0.048 2271 Dihedral : 4.578 36.605 1772 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.62 % Allowed : 17.13 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.20 (0.21), residues: 1606 helix: 1.22 (0.17), residues: 937 sheet: 0.41 (0.59), residues: 75 loop : 0.36 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 932 HIS 0.009 0.001 HIS A1444 PHE 0.010 0.001 PHE A1308 TYR 0.018 0.001 TYR A1018 ARG 0.006 0.000 ARG E 134 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 716) hydrogen bonds : angle 4.06163 ( 2025) covalent geometry : bond 0.00258 (13390) covalent geometry : angle 0.52326 (18095) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 1.467 Fit side-chains revert: symmetry clash REVERT: A 53 ASN cc_start: 0.8298 (t0) cc_final: 0.7993 (m110) REVERT: A 238 THR cc_start: 0.8871 (p) cc_final: 0.8598 (t) REVERT: A 498 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8069 (mmmt) REVERT: A 542 ILE cc_start: 0.7912 (tt) cc_final: 0.7632 (tt) REVERT: A 594 GLU cc_start: 0.8325 (mp0) cc_final: 0.7329 (mt-10) REVERT: A 596 ASP cc_start: 0.7449 (t0) cc_final: 0.7090 (m-30) REVERT: A 645 LYS cc_start: 0.8467 (tptm) cc_final: 0.8251 (tptt) REVERT: A 694 LYS cc_start: 0.8452 (ttmt) cc_final: 0.7671 (tmtt) REVERT: A 712 THR cc_start: 0.9138 (t) cc_final: 0.8741 (m) REVERT: A 728 SER cc_start: 0.8513 (p) cc_final: 0.8297 (t) REVERT: A 736 THR cc_start: 0.8953 (p) cc_final: 0.8738 (t) REVERT: A 794 ASP cc_start: 0.7803 (m-30) cc_final: 0.7544 (m-30) REVERT: A 807 LEU cc_start: 0.8304 (tp) cc_final: 0.7761 (mt) REVERT: A 1091 LYS cc_start: 0.8387 (mmmm) cc_final: 0.8072 (tppp) REVERT: A 1112 GLN cc_start: 0.8183 (tt0) cc_final: 0.7359 (pt0) REVERT: A 1133 LYS cc_start: 0.8215 (ttpt) cc_final: 0.7000 (mppt) REVERT: A 1135 GLU cc_start: 0.7902 (tp30) cc_final: 0.7616 (mm-30) REVERT: A 1225 MET cc_start: 0.8065 (ttp) cc_final: 0.7827 (ttp) REVERT: A 1246 TYR cc_start: 0.7524 (m-10) cc_final: 0.7203 (m-10) REVERT: A 1255 GLU cc_start: 0.7588 (tt0) cc_final: 0.7273 (mt-10) REVERT: A 1284 LYS cc_start: 0.8599 (ptmt) cc_final: 0.8371 (ptmm) REVERT: B 187 MET cc_start: 0.6679 (mmm) cc_final: 0.3769 (ptp) REVERT: E 195 MET cc_start: 0.6439 (ppp) cc_final: 0.5174 (tpp) outliers start: 39 outliers final: 29 residues processed: 221 average time/residue: 0.2566 time to fit residues: 84.9334 Evaluate side-chains 211 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1191 ILE Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1362 HIS Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1373 THR Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 219 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 8 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 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 248 GLN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1149 ASN A1285 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.164562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.134168 restraints weight = 14403.177| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.88 r_work: 0.3446 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13390 Z= 0.133 Angle : 0.529 7.620 18095 Z= 0.274 Chirality : 0.041 0.163 2097 Planarity : 0.003 0.049 2271 Dihedral : 4.506 35.932 1772 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.69 % Allowed : 17.13 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.24 (0.21), residues: 1606 helix: 1.24 (0.17), residues: 943 sheet: 0.32 (0.57), residues: 75 loop : 0.41 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 932 HIS 0.008 0.001 HIS A1444 PHE 0.013 0.001 PHE A 424 TYR 0.015 0.001 TYR A 746 ARG 0.005 0.000 ARG E 134 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 716) hydrogen bonds : angle 4.04178 ( 2025) covalent geometry : bond 0.00317 (13390) covalent geometry : angle 0.52875 (18095) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 1.457 Fit side-chains revert: symmetry clash REVERT: A 23 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7811 (mt) REVERT: A 238 THR cc_start: 0.8880 (p) cc_final: 0.8647 (t) REVERT: A 498 LYS cc_start: 0.8548 (mtpt) cc_final: 0.8079 (mmmt) REVERT: A 542 ILE cc_start: 0.7979 (tt) cc_final: 0.7689 (tt) REVERT: A 594 GLU cc_start: 0.8362 (mp0) cc_final: 0.7360 (mt-10) REVERT: A 596 ASP cc_start: 0.7317 (t0) cc_final: 0.6947 (m-30) REVERT: A 645 LYS cc_start: 0.8516 (tptm) cc_final: 0.8296 (tptt) REVERT: A 694 LYS cc_start: 0.8407 (ttmt) cc_final: 0.7582 (tmtt) REVERT: A 736 THR cc_start: 0.8965 (p) cc_final: 0.8713 (t) REVERT: A 794 ASP cc_start: 0.7803 (m-30) cc_final: 0.7554 (m-30) REVERT: A 807 LEU cc_start: 0.8314 (tp) cc_final: 0.7740 (mt) REVERT: A 1091 LYS cc_start: 0.8381 (mmmm) cc_final: 0.8061 (tppp) REVERT: A 1112 GLN cc_start: 0.8193 (tt0) cc_final: 0.7436 (pt0) REVERT: A 1133 LYS cc_start: 0.8226 (ttpt) cc_final: 0.6962 (mppt) REVERT: A 1225 MET cc_start: 0.8045 (ttp) cc_final: 0.7798 (ttp) REVERT: A 1246 TYR cc_start: 0.7542 (m-10) cc_final: 0.7195 (m-10) REVERT: A 1255 GLU cc_start: 0.7603 (tt0) cc_final: 0.7274 (mt-10) REVERT: A 1284 LYS cc_start: 0.8608 (ptmt) cc_final: 0.8394 (ptmm) REVERT: B 187 MET cc_start: 0.6802 (mmm) cc_final: 0.3859 (ptp) REVERT: B 195 MET cc_start: 0.7687 (mtp) cc_final: 0.7442 (mtp) REVERT: C 161 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8336 (p) REVERT: E 195 MET cc_start: 0.6448 (ppp) cc_final: 0.5209 (tpp) outliers start: 40 outliers final: 35 residues processed: 216 average time/residue: 0.2525 time to fit residues: 82.2977 Evaluate side-chains 217 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 600 CYS Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1191 ILE Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1362 HIS Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1373 THR Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain E residue 152 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 66 optimal weight: 0.0170 overall best weight: 1.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.161952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.131550 restraints weight = 14401.638| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.86 r_work: 0.3413 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13390 Z= 0.165 Angle : 0.557 8.489 18095 Z= 0.287 Chirality : 0.042 0.150 2097 Planarity : 0.003 0.048 2271 Dihedral : 4.571 36.188 1772 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.02 % Allowed : 17.46 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.20 (0.21), residues: 1606 helix: 1.23 (0.17), residues: 939 sheet: 0.21 (0.57), residues: 75 loop : 0.36 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 932 HIS 0.007 0.001 HIS A1444 PHE 0.015 0.002 PHE A 424 TYR 0.015 0.001 TYR A 86 ARG 0.008 0.000 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 716) hydrogen bonds : angle 4.10339 ( 2025) covalent geometry : bond 0.00402 (13390) covalent geometry : angle 0.55703 (18095) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.7910 (mt) REVERT: A 53 ASN cc_start: 0.8373 (t0) cc_final: 0.7957 (m110) REVERT: A 238 THR cc_start: 0.8933 (p) cc_final: 0.8730 (t) REVERT: A 498 LYS cc_start: 0.8546 (mtpt) cc_final: 0.8060 (mmmt) REVERT: A 542 ILE cc_start: 0.7990 (tt) cc_final: 0.7683 (tt) REVERT: A 594 GLU cc_start: 0.8393 (mp0) cc_final: 0.7491 (mt-10) REVERT: A 596 ASP cc_start: 0.7196 (t0) cc_final: 0.6810 (m-30) REVERT: A 645 LYS cc_start: 0.8491 (tptm) cc_final: 0.8248 (tptt) REVERT: A 694 LYS cc_start: 0.8331 (ttmt) cc_final: 0.7439 (tmtt) REVERT: A 736 THR cc_start: 0.8985 (p) cc_final: 0.8689 (t) REVERT: A 807 LEU cc_start: 0.8247 (tp) cc_final: 0.7642 (mt) REVERT: A 1091 LYS cc_start: 0.8347 (mmmm) cc_final: 0.8015 (tppp) REVERT: A 1112 GLN cc_start: 0.8259 (tt0) cc_final: 0.7453 (pt0) REVERT: A 1133 LYS cc_start: 0.8154 (ttpt) cc_final: 0.6860 (mppt) REVERT: A 1255 GLU cc_start: 0.7748 (tt0) cc_final: 0.7287 (mt-10) REVERT: A 1284 LYS cc_start: 0.8580 (ptmt) cc_final: 0.8372 (ptmm) REVERT: B 195 MET cc_start: 0.7577 (mtp) cc_final: 0.7334 (mtp) REVERT: C 161 SER cc_start: 0.8593 (OUTLIER) cc_final: 0.8231 (p) REVERT: E 195 MET cc_start: 0.6548 (ppp) cc_final: 0.5208 (tpp) outliers start: 45 outliers final: 35 residues processed: 223 average time/residue: 0.2410 time to fit residues: 80.2635 Evaluate side-chains 221 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 600 CYS Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1191 ILE Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1373 THR Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain E residue 152 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 15 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 78 optimal weight: 0.0570 chunk 141 optimal weight: 0.0270 chunk 95 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.166032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.135725 restraints weight = 14247.189| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.88 r_work: 0.3455 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13390 Z= 0.112 Angle : 0.513 8.978 18095 Z= 0.267 Chirality : 0.040 0.146 2097 Planarity : 0.003 0.050 2271 Dihedral : 4.378 35.390 1772 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.42 % Allowed : 17.93 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.39 (0.22), residues: 1606 helix: 1.39 (0.17), residues: 938 sheet: 0.04 (0.53), residues: 83 loop : 0.47 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 932 HIS 0.007 0.001 HIS A1444 PHE 0.013 0.001 PHE A1131 TYR 0.016 0.001 TYR A 86 ARG 0.004 0.000 ARG E 134 Details of bonding type rmsd hydrogen bonds : bond 0.03149 ( 716) hydrogen bonds : angle 3.99307 ( 2025) covalent geometry : bond 0.00261 (13390) covalent geometry : angle 0.51328 (18095) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASN cc_start: 0.8425 (t0) cc_final: 0.8008 (m110) REVERT: A 190 LEU cc_start: 0.8740 (mm) cc_final: 0.8446 (mt) REVERT: A 220 GLN cc_start: 0.7793 (mt0) cc_final: 0.7550 (mt0) REVERT: A 238 THR cc_start: 0.8840 (p) cc_final: 0.8584 (t) REVERT: A 421 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6516 (tt0) REVERT: A 498 LYS cc_start: 0.8539 (mtpt) cc_final: 0.8056 (mmmt) REVERT: A 542 ILE cc_start: 0.7901 (tt) cc_final: 0.7595 (tt) REVERT: A 594 GLU cc_start: 0.8350 (mp0) cc_final: 0.7295 (mt-10) REVERT: A 596 ASP cc_start: 0.7046 (t0) cc_final: 0.6635 (m-30) REVERT: A 645 LYS cc_start: 0.8440 (tptm) cc_final: 0.8226 (tptt) REVERT: A 694 LYS cc_start: 0.8353 (ttmt) cc_final: 0.7438 (tmtt) REVERT: A 700 ASP cc_start: 0.8242 (t0) cc_final: 0.8037 (t0) REVERT: A 736 THR cc_start: 0.8967 (p) cc_final: 0.8669 (t) REVERT: A 807 LEU cc_start: 0.8238 (tp) cc_final: 0.7669 (mt) REVERT: A 866 MET cc_start: 0.7701 (tpp) cc_final: 0.7367 (tpp) REVERT: A 1091 LYS cc_start: 0.8338 (mmmm) cc_final: 0.8003 (tppp) REVERT: A 1112 GLN cc_start: 0.8234 (tt0) cc_final: 0.7437 (pt0) REVERT: A 1133 LYS cc_start: 0.8172 (ttpt) cc_final: 0.6861 (mppt) REVERT: A 1225 MET cc_start: 0.8099 (ttp) cc_final: 0.7777 (ttp) REVERT: A 1255 GLU cc_start: 0.7671 (tt0) cc_final: 0.7320 (mt-10) REVERT: A 1284 LYS cc_start: 0.8594 (ptmt) cc_final: 0.8378 (ptmm) REVERT: B 187 MET cc_start: 0.6880 (mmm) cc_final: 0.4058 (ptp) REVERT: B 195 MET cc_start: 0.7562 (mtp) cc_final: 0.7339 (mtp) REVERT: C 161 SER cc_start: 0.8598 (OUTLIER) cc_final: 0.8252 (p) REVERT: E 195 MET cc_start: 0.6537 (ppp) cc_final: 0.5240 (tpp) outliers start: 36 outliers final: 30 residues processed: 227 average time/residue: 0.2480 time to fit residues: 83.8224 Evaluate side-chains 221 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1191 ILE Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1373 THR Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain E residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 102 optimal weight: 0.5980 chunk 99 optimal weight: 0.3980 chunk 24 optimal weight: 0.0870 chunk 23 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A1330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.165687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.136138 restraints weight = 14162.149| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.83 r_work: 0.3474 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13390 Z= 0.110 Angle : 0.522 11.494 18095 Z= 0.269 Chirality : 0.040 0.144 2097 Planarity : 0.003 0.052 2271 Dihedral : 4.300 34.079 1772 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.15 % Allowed : 18.20 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.47 (0.22), residues: 1606 helix: 1.47 (0.17), residues: 937 sheet: 0.10 (0.54), residues: 83 loop : 0.48 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 932 HIS 0.007 0.001 HIS A1444 PHE 0.014 0.001 PHE A1131 TYR 0.015 0.001 TYR A 86 ARG 0.004 0.000 ARG E 134 Details of bonding type rmsd hydrogen bonds : bond 0.03106 ( 716) hydrogen bonds : angle 3.96102 ( 2025) covalent geometry : bond 0.00252 (13390) covalent geometry : angle 0.52186 (18095) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASN cc_start: 0.8379 (t0) cc_final: 0.8077 (m110) REVERT: A 190 LEU cc_start: 0.8751 (mm) cc_final: 0.8449 (mt) REVERT: A 421 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6517 (tt0) REVERT: A 498 LYS cc_start: 0.8554 (mtpt) cc_final: 0.8088 (mmmt) REVERT: A 542 ILE cc_start: 0.7951 (tt) cc_final: 0.7674 (tt) REVERT: A 594 GLU cc_start: 0.8426 (mp0) cc_final: 0.7470 (mt-10) REVERT: A 596 ASP cc_start: 0.7235 (t0) cc_final: 0.6837 (m-30) REVERT: A 694 LYS cc_start: 0.8385 (ttmt) cc_final: 0.7510 (tmtt) REVERT: A 736 THR cc_start: 0.8943 (p) cc_final: 0.8652 (t) REVERT: A 807 LEU cc_start: 0.8337 (tp) cc_final: 0.7790 (mt) REVERT: A 866 MET cc_start: 0.7666 (tpp) cc_final: 0.7333 (tpp) REVERT: A 1091 LYS cc_start: 0.8378 (mmmm) cc_final: 0.8056 (tppp) REVERT: A 1098 GLN cc_start: 0.8540 (mt0) cc_final: 0.8337 (mt0) REVERT: A 1112 GLN cc_start: 0.8168 (tt0) cc_final: 0.7479 (pt0) REVERT: A 1133 LYS cc_start: 0.8215 (ttpt) cc_final: 0.6921 (mtmm) REVERT: A 1152 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8113 (mm-30) REVERT: A 1246 TYR cc_start: 0.7529 (m-10) cc_final: 0.7155 (m-10) REVERT: A 1255 GLU cc_start: 0.7592 (tt0) cc_final: 0.7320 (mt-10) REVERT: A 1284 LYS cc_start: 0.8647 (ptmt) cc_final: 0.8443 (ptmm) REVERT: A 1304 ASN cc_start: 0.7251 (p0) cc_final: 0.7004 (p0) REVERT: B 187 MET cc_start: 0.7021 (mmm) cc_final: 0.4269 (ptp) REVERT: C 161 SER cc_start: 0.8716 (OUTLIER) cc_final: 0.8412 (p) REVERT: E 195 MET cc_start: 0.6596 (ppp) cc_final: 0.5322 (tpp) outliers start: 32 outliers final: 28 residues processed: 222 average time/residue: 0.2917 time to fit residues: 96.2618 Evaluate side-chains 217 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 600 CYS Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1373 THR Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain E residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 101 optimal weight: 0.6980 chunk 2 optimal weight: 0.0470 chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 53 optimal weight: 0.0370 chunk 154 optimal weight: 20.0000 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A1417 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.166236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.138055 restraints weight = 14294.860| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.76 r_work: 0.3396 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13390 Z= 0.115 Angle : 0.533 16.119 18095 Z= 0.272 Chirality : 0.040 0.145 2097 Planarity : 0.003 0.051 2271 Dihedral : 4.264 33.341 1772 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.08 % Allowed : 18.74 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.51 (0.22), residues: 1606 helix: 1.50 (0.17), residues: 939 sheet: 0.15 (0.54), residues: 83 loop : 0.48 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 932 HIS 0.007 0.001 HIS A1444 PHE 0.012 0.001 PHE A1131 TYR 0.014 0.001 TYR A 746 ARG 0.004 0.000 ARG E 134 Details of bonding type rmsd hydrogen bonds : bond 0.03084 ( 716) hydrogen bonds : angle 3.93702 ( 2025) covalent geometry : bond 0.00269 (13390) covalent geometry : angle 0.53282 (18095) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8188.87 seconds wall clock time: 143 minutes 50.87 seconds (8630.87 seconds total)