Starting phenix.real_space_refine on Fri Aug 22 20:03:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pzc_20534/08_2025/6pzc_20534_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pzc_20534/08_2025/6pzc_20534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pzc_20534/08_2025/6pzc_20534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pzc_20534/08_2025/6pzc_20534.map" model { file = "/net/cci-nas-00/data/ceres_data/6pzc_20534/08_2025/6pzc_20534_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pzc_20534/08_2025/6pzc_20534_neut.cif" } resolution = 4.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 20 5.16 5 C 4723 2.51 5 N 1354 2.21 5 O 1359 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7456 Number of models: 1 Model: "" Number of chains: 1 Chain: "H" Number of atoms: 7456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1173, 7456 Classifications: {'peptide': 1173} Incomplete info: {'truncation_to_alanine': 541} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 36, 'TRANS': 1134} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1772 Unresolved non-hydrogen angles: 2243 Unresolved non-hydrogen dihedrals: 1389 Unresolved non-hydrogen chiralities: 234 Planarities with less than four sites: {'ASP:plan': 35, 'ARG:plan': 31, 'GLN:plan1': 33, 'GLU:plan': 36, 'PHE:plan': 21, 'ASN:plan1': 20, 'TYR:plan': 4, 'TRP:plan': 3, 'HIS:plan': 6} Unresolved non-hydrogen planarities: 807 Time building chain proxies: 2.11, per 1000 atoms: 0.28 Number of scatterers: 7456 At special positions: 0 Unit cell: (84.28, 94.6, 135.88, 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 20 16.00 O 1359 8.00 N 1354 7.00 C 4723 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 403.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2226 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 5 sheets defined 66.7% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'H' and resid 223 through 230 Processing helix chain 'H' and resid 231 through 243 removed outlier: 4.275A pdb=" N ALA H 235 " --> pdb=" O TRP H 231 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE H 236 " --> pdb=" O TRP H 232 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS H 242 " --> pdb=" O LYS H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 274 removed outlier: 3.608A pdb=" N ASN H 262 " --> pdb=" O ARG H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 327 removed outlier: 3.521A pdb=" N ARG H 289 " --> pdb=" O ARG H 285 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS H 293 " --> pdb=" O ARG H 289 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ARG H 297 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG H 298 " --> pdb=" O ALA H 294 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA H 315 " --> pdb=" O LEU H 311 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY H 316 " --> pdb=" O LEU H 312 " (cutoff:3.500A) Proline residue: H 317 - end of helix Processing helix chain 'H' and resid 347 through 352 Processing helix chain 'H' and resid 354 through 400 removed outlier: 3.951A pdb=" N LEU H 368 " --> pdb=" O LEU H 364 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU H 373 " --> pdb=" O GLN H 369 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLN H 374 " --> pdb=" O ARG H 370 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR H 378 " --> pdb=" O GLN H 374 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA H 380 " --> pdb=" O SER H 376 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ASN H 386 " --> pdb=" O GLU H 382 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY H 389 " --> pdb=" O ILE H 385 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA H 390 " --> pdb=" O ASN H 386 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS H 394 " --> pdb=" O ALA H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 413 through 423 removed outlier: 3.896A pdb=" N LEU H 420 " --> pdb=" O GLN H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 423 through 454 Proline residue: H 436 - end of helix removed outlier: 3.851A pdb=" N TRP H 439 " --> pdb=" O CYS H 435 " (cutoff:3.500A) Proline residue: H 442 - end of helix Processing helix chain 'H' and resid 457 through 471 removed outlier: 3.831A pdb=" N ALA H 465 " --> pdb=" O LEU H 461 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N VAL H 466 " --> pdb=" O ILE H 462 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE H 467 " --> pdb=" O GLY H 463 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA H 471 " --> pdb=" O ILE H 467 " (cutoff:3.500A) Processing helix chain 'H' and resid 471 through 505 removed outlier: 3.809A pdb=" N TYR H 475 " --> pdb=" O ALA H 471 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR H 479 " --> pdb=" O TYR H 475 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS H 480 " --> pdb=" O PHE H 476 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLU H 494 " --> pdb=" O GLU H 490 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG H 495 " --> pdb=" O HIS H 491 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY H 505 " --> pdb=" O GLU H 501 " (cutoff:3.500A) Processing helix chain 'H' and resid 505 through 512 Processing helix chain 'H' and resid 514 through 564 removed outlier: 3.684A pdb=" N PHE H 518 " --> pdb=" O TRP H 514 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL H 522 " --> pdb=" O PHE H 518 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS H 528 " --> pdb=" O VAL H 524 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA H 535 " --> pdb=" O THR H 531 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE H 542 " --> pdb=" O VAL H 538 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER H 543 " --> pdb=" O TYR H 539 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE H 544 " --> pdb=" O THR H 540 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE H 550 " --> pdb=" O MET H 546 " (cutoff:3.500A) Proline residue: H 551 - end of helix removed outlier: 3.643A pdb=" N ILE H 557 " --> pdb=" O ALA H 553 " (cutoff:3.500A) Processing helix chain 'H' and resid 572 through 591 removed outlier: 3.529A pdb=" N LEU H 580 " --> pdb=" O ALA H 576 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL H 587 " --> pdb=" O PHE H 583 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THR H 588 " --> pdb=" O HIS H 584 " (cutoff:3.500A) Proline residue: H 589 - end of helix Processing helix chain 'H' and resid 592 through 615 removed outlier: 3.838A pdb=" N GLN H 608 " --> pdb=" O LEU H 604 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE H 613 " --> pdb=" O LYS H 609 " (cutoff:3.500A) Processing helix chain 'H' and resid 720 through 728 removed outlier: 3.549A pdb=" N GLY H 728 " --> pdb=" O LEU H 724 " (cutoff:3.500A) Processing helix chain 'H' and resid 783 through 790 Processing helix chain 'H' and resid 795 through 807 removed outlier: 4.756A pdb=" N ALA H 805 " --> pdb=" O MET H 801 " (cutoff:3.500A) Processing helix chain 'H' and resid 808 through 815 Processing helix chain 'H' and resid 817 through 821 Processing helix chain 'H' and resid 834 through 846 Processing helix chain 'H' and resid 855 through 860 removed outlier: 3.928A pdb=" N ALA H 859 " --> pdb=" O ASP H 855 " (cutoff:3.500A) Processing helix chain 'H' and resid 861 through 879 Processing helix chain 'H' and resid 918 through 923 removed outlier: 3.997A pdb=" N CYS H 922 " --> pdb=" O GLN H 918 " (cutoff:3.500A) Processing helix chain 'H' and resid 996 through 1004 removed outlier: 3.993A pdb=" N ALA H1000 " --> pdb=" O ILE H 996 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N CYS H1001 " --> pdb=" O PRO H 997 " (cutoff:3.500A) Processing helix chain 'H' and resid 1009 through 1044 removed outlier: 3.819A pdb=" N GLN H1020 " --> pdb=" O LEU H1016 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS H1024 " --> pdb=" O GLN H1020 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA H1029 " --> pdb=" O MET H1025 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS H1036 " --> pdb=" O TYR H1032 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR H1038 " --> pdb=" O LEU H1034 " (cutoff:3.500A) Processing helix chain 'H' and resid 1060 through 1107 removed outlier: 3.741A pdb=" N MET H1066 " --> pdb=" O SER H1062 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL H1067 " --> pdb=" O VAL H1063 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY H1075 " --> pdb=" O LEU H1071 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE H1076 " --> pdb=" O CYS H1072 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU H1080 " --> pdb=" O ILE H1076 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL H1081 " --> pdb=" O VAL H1077 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL H1086 " --> pdb=" O THR H1082 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU H1087 " --> pdb=" O SER H1083 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU H1107 " --> pdb=" O ASN H1103 " (cutoff:3.500A) Processing helix chain 'H' and resid 1109 through 1116 removed outlier: 3.661A pdb=" N PHE H1113 " --> pdb=" O PRO H1109 " (cutoff:3.500A) Processing helix chain 'H' and resid 1117 through 1135 removed outlier: 3.608A pdb=" N ILE H1121 " --> pdb=" O PRO H1117 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG H1124 " --> pdb=" O SER H1120 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER H1127 " --> pdb=" O ASN H1123 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP H1128 " --> pdb=" O ARG H1124 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N CYS H1129 " --> pdb=" O PHE H1125 " (cutoff:3.500A) Processing helix chain 'H' and resid 1136 through 1161 removed outlier: 3.774A pdb=" N LEU H1140 " --> pdb=" O ILE H1136 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU H1148 " --> pdb=" O SER H1144 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU H1149 " --> pdb=" O ARG H1145 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU H1154 " --> pdb=" O CYS H1150 " (cutoff:3.500A) Processing helix chain 'H' and resid 1164 through 1195 Proline residue: H1170 - end of helix removed outlier: 3.606A pdb=" N VAL H1173 " --> pdb=" O LEU H1169 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL H1174 " --> pdb=" O PRO H1170 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL H1184 " --> pdb=" O LYS H1180 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA H1185 " --> pdb=" O TYR H1181 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG H1187 " --> pdb=" O ARG H1183 " (cutoff:3.500A) Processing helix chain 'H' and resid 1196 through 1210 removed outlier: 3.720A pdb=" N LEU H1200 " --> pdb=" O THR H1196 " (cutoff:3.500A) Processing helix chain 'H' and resid 1210 through 1218 removed outlier: 3.557A pdb=" N ILE H1214 " --> pdb=" O GLY H1210 " (cutoff:3.500A) Processing helix chain 'H' and resid 1219 through 1267 removed outlier: 3.613A pdb=" N TYR H1230 " --> pdb=" O LYS H1226 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER H1233 " --> pdb=" O GLU H1229 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU H1249 " --> pdb=" O ASN H1245 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE H1255 " --> pdb=" O CYS H1251 " (cutoff:3.500A) Processing helix chain 'H' and resid 1268 through 1271 Processing helix chain 'H' and resid 1278 through 1289 removed outlier: 3.971A pdb=" N GLY H1282 " --> pdb=" O ALA H1278 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU H1283 " --> pdb=" O GLY H1279 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY H1284 " --> pdb=" O LEU H1280 " (cutoff:3.500A) Processing helix chain 'H' and resid 1290 through 1313 removed outlier: 4.203A pdb=" N TYR H1294 " --> pdb=" O MET H1290 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL H1299 " --> pdb=" O LEU H1295 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG H1300 " --> pdb=" O ASN H1296 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU H1302 " --> pdb=" O MET H1298 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU H1306 " --> pdb=" O LEU H1302 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE H1307 " --> pdb=" O ALA H1303 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA H1311 " --> pdb=" O ILE H1307 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL H1312 " --> pdb=" O GLN H1308 " (cutoff:3.500A) Processing helix chain 'H' and resid 1313 through 1319 removed outlier: 4.024A pdb=" N ALA H1317 " --> pdb=" O LYS H1313 " (cutoff:3.500A) Processing helix chain 'H' and resid 1414 through 1419 Processing helix chain 'H' and resid 1436 through 1441 Processing helix chain 'H' and resid 1450 through 1458 removed outlier: 3.874A pdb=" N LEU H1455 " --> pdb=" O LEU H1451 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU H1456 " --> pdb=" O TRP H1452 " (cutoff:3.500A) Processing helix chain 'H' and resid 1469 through 1472 Processing helix chain 'H' and resid 1476 through 1479 removed outlier: 3.758A pdb=" N GLY H1479 " --> pdb=" O THR H1476 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1476 through 1479' Processing helix chain 'H' and resid 1485 through 1498 removed outlier: 3.597A pdb=" N CYS H1491 " --> pdb=" O ARG H1487 " (cutoff:3.500A) Processing helix chain 'H' and resid 1513 through 1526 Processing helix chain 'H' and resid 1539 through 1546 removed outlier: 3.627A pdb=" N THR H1542 " --> pdb=" O ARG H1539 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER H1545 " --> pdb=" O THR H1542 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 696 through 703 removed outlier: 4.978A pdb=" N GLY H 684 " --> pdb=" O ASN H 698 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR H 700 " --> pdb=" O ILE H 682 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE H 682 " --> pdb=" O THR H 700 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG H 702 " --> pdb=" O GLN H 680 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLN H 680 " --> pdb=" O ARG H 702 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 1365 through 1368 removed outlier: 4.539A pdb=" N VAL H1365 " --> pdb=" O ASN H1349 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN H1349 " --> pdb=" O GLY H1401 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY H1401 " --> pdb=" O ASN H1349 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER H1351 " --> pdb=" O PHE H1399 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 1376 through 1377 Processing sheet with id=AA4, first strand: chain 'H' and resid 1404 through 1405 Processing sheet with id=AA5, first strand: chain 'H' and resid 1434 through 1435 503 hydrogen bonds defined for protein. 1473 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: 1.14 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2219 1.33 - 1.45: 1277 1.45 - 1.57: 4065 1.57 - 1.69: 0 1.69 - 1.81: 29 Bond restraints: 7590 Sorted by residual: bond pdb=" C GLU H 382 " pdb=" N THR H 383 " ideal model delta sigma weight residual 1.324 1.218 0.106 2.56e-02 1.53e+03 1.72e+01 bond pdb=" CB TYR H 396 " pdb=" CG TYR H 396 " ideal model delta sigma weight residual 1.512 1.457 0.055 2.20e-02 2.07e+03 6.27e+00 bond pdb=" N THR H 383 " pdb=" CA THR H 383 " ideal model delta sigma weight residual 1.459 1.428 0.030 1.41e-02 5.03e+03 4.63e+00 bond pdb=" CB TRP H 739 " pdb=" CG TRP H 739 " ideal model delta sigma weight residual 1.498 1.432 0.066 3.10e-02 1.04e+03 4.59e+00 bond pdb=" CB TRP H1037 " pdb=" CG TRP H1037 " ideal model delta sigma weight residual 1.498 1.433 0.065 3.10e-02 1.04e+03 4.38e+00 ... (remaining 7585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 10040 2.49 - 4.97: 341 4.97 - 7.46: 53 7.46 - 9.95: 15 9.95 - 12.44: 4 Bond angle restraints: 10453 Sorted by residual: angle pdb=" C PRO H 281 " pdb=" N GLN H 282 " pdb=" CA GLN H 282 " ideal model delta sigma weight residual 121.70 131.19 -9.49 1.80e+00 3.09e-01 2.78e+01 angle pdb=" C ASN H1338 " pdb=" N TRP H1339 " pdb=" CA TRP H1339 " ideal model delta sigma weight residual 121.80 132.35 -10.55 2.44e+00 1.68e-01 1.87e+01 angle pdb=" CA TRP H1297 " pdb=" CB TRP H1297 " pdb=" CG TRP H1297 " ideal model delta sigma weight residual 113.60 121.62 -8.02 1.90e+00 2.77e-01 1.78e+01 angle pdb=" CB MET H 441 " pdb=" CG MET H 441 " pdb=" SD MET H 441 " ideal model delta sigma weight residual 112.70 100.26 12.44 3.00e+00 1.11e-01 1.72e+01 angle pdb=" N THR H 383 " pdb=" CA THR H 383 " pdb=" C THR H 383 " ideal model delta sigma weight residual 113.18 107.69 5.49 1.33e+00 5.65e-01 1.70e+01 ... (remaining 10448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 4135 15.06 - 30.12: 234 30.12 - 45.18: 43 45.18 - 60.25: 5 60.25 - 75.31: 2 Dihedral angle restraints: 4419 sinusoidal: 1003 harmonic: 3416 Sorted by residual: dihedral pdb=" CA TRP H1339 " pdb=" C TRP H1339 " pdb=" N PRO H1340 " pdb=" CA PRO H1340 " ideal model delta harmonic sigma weight residual -180.00 -127.26 -52.74 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA THR H 229 " pdb=" C THR H 229 " pdb=" N TYR H 230 " pdb=" CA TYR H 230 " ideal model delta harmonic sigma weight residual 180.00 141.11 38.89 0 5.00e+00 4.00e-02 6.05e+01 dihedral pdb=" CA ASN H 223 " pdb=" C ASN H 223 " pdb=" N LEU H 224 " pdb=" CA LEU H 224 " ideal model delta harmonic sigma weight residual -180.00 -146.66 -33.34 0 5.00e+00 4.00e-02 4.45e+01 ... (remaining 4416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1103 0.080 - 0.159: 176 0.159 - 0.239: 11 0.239 - 0.319: 4 0.319 - 0.398: 1 Chirality restraints: 1295 Sorted by residual: chirality pdb=" CB ILE H1255 " pdb=" CA ILE H1255 " pdb=" CG1 ILE H1255 " pdb=" CG2 ILE H1255 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CA ARG H 826 " pdb=" N ARG H 826 " pdb=" C ARG H 826 " pdb=" CB ARG H 826 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA PHE H1223 " pdb=" N PHE H1223 " pdb=" C PHE H1223 " pdb=" CB PHE H1223 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 1292 not shown) Planarity restraints: 1380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR H1242 " -0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C THR H1242 " 0.077 2.00e-02 2.50e+03 pdb=" O THR H1242 " -0.029 2.00e-02 2.50e+03 pdb=" N ALA H1243 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H1233 " 0.021 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C SER H1233 " -0.073 2.00e-02 2.50e+03 pdb=" O SER H1233 " 0.028 2.00e-02 2.50e+03 pdb=" N ASN H1234 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 232 " 0.039 2.00e-02 2.50e+03 2.38e-02 1.41e+01 pdb=" CG TRP H 232 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP H 232 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP H 232 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP H 232 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP H 232 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP H 232 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 232 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 232 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP H 232 " 0.006 2.00e-02 2.50e+03 ... (remaining 1377 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 267 2.69 - 3.24: 8109 3.24 - 3.79: 12518 3.79 - 4.35: 14421 4.35 - 4.90: 21770 Nonbonded interactions: 57085 Sorted by model distance: nonbonded pdb=" NZ LYS H 398 " pdb=" O LEU H 614 " model vdw 2.137 3.120 nonbonded pdb=" N ASN H 781 " pdb=" OE2 GLU H1206 " model vdw 2.154 3.120 nonbonded pdb=" O LEU H1192 " pdb=" OG1 THR H1196 " model vdw 2.211 3.040 nonbonded pdb=" O LEU H 367 " pdb=" OG1 THR H 371 " model vdw 2.234 3.040 nonbonded pdb=" O LEU H1148 " pdb=" OG SER H1152 " model vdw 2.247 3.040 ... (remaining 57080 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.550 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5686 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 : 0.008 0.106 7590 Z= 0.432 Angle : 1.122 12.437 10453 Z= 0.640 Chirality : 0.058 0.398 1295 Planarity : 0.010 0.093 1380 Dihedral : 11.224 75.307 2193 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 0.42 % Allowed : 6.96 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.09 % Twisted Proline : 2.70 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.15 (0.18), residues: 1159 helix: -2.94 (0.13), residues: 712 sheet: -5.31 (0.48), residues: 19 loop : -3.97 (0.25), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG H 370 TYR 0.043 0.004 TYR H 475 PHE 0.033 0.004 PHE H 270 TRP 0.062 0.005 TRP H 232 HIS 0.010 0.004 HIS H 584 Details of bonding type rmsd covalent geometry : bond 0.00832 ( 7590) covalent geometry : angle 1.12182 (10453) hydrogen bonds : bond 0.18433 ( 503) hydrogen bonds : angle 8.23710 ( 1473) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 363 PHE cc_start: 0.7585 (t80) cc_final: 0.7239 (t80) REVERT: H 367 LEU cc_start: 0.8209 (mt) cc_final: 0.7865 (mt) REVERT: H 445 ILE cc_start: 0.8403 (mt) cc_final: 0.8018 (mt) REVERT: H 1121 ILE cc_start: 0.7685 (mt) cc_final: 0.7309 (mp) REVERT: H 1214 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7116 (mp) outliers start: 2 outliers final: 0 residues processed: 161 average time/residue: 0.0698 time to fit residues: 15.1305 Evaluate side-chains 106 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.0870 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 30.0000 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 262 ASN H 386 ASN H 491 HIS H1179 GLN ** H1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.078369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.061271 restraints weight = 32975.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.063111 restraints weight = 22072.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.064534 restraints weight = 16136.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.065643 restraints weight = 12367.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.066393 restraints weight = 9937.687| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.5920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 7590 Z= 0.290 Angle : 0.854 12.316 10453 Z= 0.464 Chirality : 0.048 0.316 1295 Planarity : 0.007 0.093 1380 Dihedral : 6.123 45.235 1218 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 1.05 % Allowed : 4.01 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.09 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.94 (0.22), residues: 1159 helix: -0.89 (0.17), residues: 751 sheet: -5.20 (0.52), residues: 21 loop : -3.85 (0.27), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 598 TYR 0.033 0.004 TYR H1254 PHE 0.030 0.003 PHE H 270 TRP 0.080 0.005 TRP H 430 HIS 0.011 0.003 HIS H 491 Details of bonding type rmsd covalent geometry : bond 0.00591 ( 7590) covalent geometry : angle 0.85421 (10453) hydrogen bonds : bond 0.05084 ( 503) hydrogen bonds : angle 6.02654 ( 1473) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 168 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 264 GLN cc_start: 0.9202 (tp-100) cc_final: 0.8685 (tp-100) REVERT: H 268 VAL cc_start: 0.9242 (t) cc_final: 0.8644 (t) REVERT: H 363 PHE cc_start: 0.7653 (t80) cc_final: 0.7274 (t80) REVERT: H 367 LEU cc_start: 0.9608 (mt) cc_final: 0.9300 (mt) REVERT: H 387 LEU cc_start: 0.8387 (mt) cc_final: 0.8059 (mt) REVERT: H 412 MET cc_start: 0.8280 (mpp) cc_final: 0.7762 (tpp) REVERT: H 418 CYS cc_start: 0.9231 (t) cc_final: 0.8743 (p) REVERT: H 421 VAL cc_start: 0.8606 (t) cc_final: 0.8366 (m) REVERT: H 445 ILE cc_start: 0.9407 (mt) cc_final: 0.9174 (mm) REVERT: H 485 GLN cc_start: 0.8544 (pt0) cc_final: 0.8163 (pt0) REVERT: H 595 SER cc_start: 0.8136 (p) cc_final: 0.7854 (t) REVERT: H 602 LYS cc_start: 0.8788 (mmtm) cc_final: 0.8430 (mmtm) REVERT: H 609 LYS cc_start: 0.9267 (mmtm) cc_final: 0.8900 (mmmt) REVERT: H 1127 SER cc_start: 0.8018 (t) cc_final: 0.7807 (m) REVERT: H 1139 THR cc_start: 0.8870 (m) cc_final: 0.7993 (t) REVERT: H 1202 SER cc_start: 0.8440 (m) cc_final: 0.8072 (t) REVERT: H 1209 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7407 (tt0) REVERT: H 1223 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.8236 (m-10) REVERT: H 1280 LEU cc_start: 0.8876 (mt) cc_final: 0.8571 (tp) outliers start: 5 outliers final: 1 residues processed: 172 average time/residue: 0.0503 time to fit residues: 12.5976 Evaluate side-chains 131 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 62 optimal weight: 0.2980 chunk 94 optimal weight: 30.0000 chunk 98 optimal weight: 0.0770 chunk 34 optimal weight: 0.9980 chunk 104 optimal weight: 0.0970 chunk 44 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 overall best weight: 0.8938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 444 GLN H1301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.079558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.062327 restraints weight = 32179.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.064283 restraints weight = 21443.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.065723 restraints weight = 15509.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.066700 restraints weight = 11894.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.067609 restraints weight = 9636.940| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.7032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7590 Z= 0.127 Angle : 0.599 9.037 10453 Z= 0.314 Chirality : 0.042 0.155 1295 Planarity : 0.005 0.090 1380 Dihedral : 5.201 44.460 1218 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.21 % Allowed : 3.38 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.09 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.24), residues: 1159 helix: 0.45 (0.19), residues: 749 sheet: -5.02 (0.58), residues: 21 loop : -3.72 (0.27), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 486 TYR 0.015 0.001 TYR H 263 PHE 0.021 0.002 PHE H1223 TRP 0.040 0.002 TRP H 430 HIS 0.007 0.001 HIS H 867 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 7590) covalent geometry : angle 0.59935 (10453) hydrogen bonds : bond 0.03846 ( 503) hydrogen bonds : angle 4.93887 ( 1473) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 264 GLN cc_start: 0.9220 (tp-100) cc_final: 0.8748 (tp-100) REVERT: H 304 THR cc_start: 0.9292 (m) cc_final: 0.9083 (p) REVERT: H 363 PHE cc_start: 0.8042 (t80) cc_final: 0.7385 (t80) REVERT: H 367 LEU cc_start: 0.9606 (mt) cc_final: 0.9321 (mt) REVERT: H 412 MET cc_start: 0.8348 (mpp) cc_final: 0.7867 (tpt) REVERT: H 418 CYS cc_start: 0.9091 (t) cc_final: 0.8391 (p) REVERT: H 441 MET cc_start: 0.9088 (tpp) cc_final: 0.8719 (tpp) REVERT: H 445 ILE cc_start: 0.9284 (mt) cc_final: 0.9075 (mm) REVERT: H 544 ILE cc_start: 0.9369 (mm) cc_final: 0.9157 (mm) REVERT: H 602 LYS cc_start: 0.8920 (mmtm) cc_final: 0.8513 (mmtm) REVERT: H 609 LYS cc_start: 0.9499 (mmtm) cc_final: 0.9231 (mmmm) REVERT: H 1139 THR cc_start: 0.9019 (m) cc_final: 0.8484 (t) REVERT: H 1180 LYS cc_start: 0.7858 (ttpt) cc_final: 0.7582 (mttt) REVERT: H 1202 SER cc_start: 0.8623 (m) cc_final: 0.8221 (t) REVERT: H 1225 GLN cc_start: 0.8393 (mt0) cc_final: 0.8161 (mt0) REVERT: H 1248 LEU cc_start: 0.8905 (tp) cc_final: 0.8455 (tp) REVERT: H 1280 LEU cc_start: 0.9145 (mt) cc_final: 0.8824 (tp) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.0477 time to fit residues: 10.8941 Evaluate side-chains 128 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 30 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 101 optimal weight: 0.4980 chunk 1 optimal weight: 0.0040 chunk 60 optimal weight: 0.0060 chunk 59 optimal weight: 20.0000 overall best weight: 0.4808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 234 ASN H 444 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.080057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.062883 restraints weight = 32433.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.064773 restraints weight = 21827.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.066182 restraints weight = 15866.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.067272 restraints weight = 12199.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.068091 restraints weight = 9753.742| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.7675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7590 Z= 0.108 Angle : 0.547 8.702 10453 Z= 0.284 Chirality : 0.041 0.160 1295 Planarity : 0.004 0.087 1380 Dihedral : 4.623 43.651 1218 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.09 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.25), residues: 1159 helix: 1.14 (0.19), residues: 743 sheet: -4.28 (0.64), residues: 38 loop : -3.42 (0.27), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 486 TYR 0.022 0.002 TYR H1254 PHE 0.017 0.002 PHE H1177 TRP 0.017 0.001 TRP H 232 HIS 0.007 0.001 HIS H 867 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 7590) covalent geometry : angle 0.54709 (10453) hydrogen bonds : bond 0.03418 ( 503) hydrogen bonds : angle 4.40473 ( 1473) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 237 ILE cc_start: 0.8778 (pt) cc_final: 0.7960 (pt) REVERT: H 267 CYS cc_start: 0.9131 (m) cc_final: 0.8879 (m) REVERT: H 304 THR cc_start: 0.9317 (m) cc_final: 0.9085 (p) REVERT: H 314 PHE cc_start: 0.7844 (m-80) cc_final: 0.5356 (m-80) REVERT: H 323 ILE cc_start: 0.9583 (mm) cc_final: 0.9365 (mm) REVERT: H 363 PHE cc_start: 0.8084 (t80) cc_final: 0.7471 (t80) REVERT: H 367 LEU cc_start: 0.9432 (mt) cc_final: 0.9078 (mt) REVERT: H 374 GLN cc_start: 0.9090 (mm-40) cc_final: 0.8831 (mm110) REVERT: H 412 MET cc_start: 0.8224 (mpp) cc_final: 0.7605 (tpp) REVERT: H 418 CYS cc_start: 0.9230 (t) cc_final: 0.8773 (p) REVERT: H 473 VAL cc_start: 0.9073 (t) cc_final: 0.8716 (m) REVERT: H 544 ILE cc_start: 0.9202 (mm) cc_final: 0.8973 (mm) REVERT: H 580 LEU cc_start: 0.9183 (tp) cc_final: 0.8945 (tp) REVERT: H 609 LYS cc_start: 0.9558 (mmtm) cc_final: 0.9248 (mmmm) REVERT: H 1139 THR cc_start: 0.9049 (m) cc_final: 0.8555 (t) REVERT: H 1140 LEU cc_start: 0.9264 (mt) cc_final: 0.8740 (mt) REVERT: H 1148 LEU cc_start: 0.9332 (mt) cc_final: 0.9057 (mt) REVERT: H 1177 PHE cc_start: 0.6714 (t80) cc_final: 0.6397 (t80) REVERT: H 1180 LYS cc_start: 0.7936 (ttpt) cc_final: 0.7575 (mttt) REVERT: H 1181 TYR cc_start: 0.8354 (m-10) cc_final: 0.8100 (m-10) REVERT: H 1202 SER cc_start: 0.8679 (m) cc_final: 0.8374 (t) REVERT: H 1225 GLN cc_start: 0.8326 (mt0) cc_final: 0.8040 (mt0) REVERT: H 1239 LEU cc_start: 0.8811 (mm) cc_final: 0.8257 (tp) REVERT: H 1247 TRP cc_start: 0.9234 (t60) cc_final: 0.8744 (t60) REVERT: H 1306 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7546 (mp0) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.0600 time to fit residues: 13.8736 Evaluate side-chains 134 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 109 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 62 optimal weight: 0.0970 chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.077205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.060353 restraints weight = 33528.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.062165 restraints weight = 22610.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.063328 restraints weight = 16483.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.064449 restraints weight = 13065.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.065058 restraints weight = 10482.633| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.9437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7590 Z= 0.174 Angle : 0.637 13.517 10453 Z= 0.333 Chirality : 0.043 0.153 1295 Planarity : 0.005 0.082 1380 Dihedral : 4.702 41.569 1218 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.09 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.26), residues: 1159 helix: 1.21 (0.20), residues: 738 sheet: -5.15 (0.79), residues: 22 loop : -3.10 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 388 TYR 0.017 0.002 TYR H 396 PHE 0.031 0.003 PHE H 591 TRP 0.016 0.002 TRP H 232 HIS 0.007 0.001 HIS H 867 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7590) covalent geometry : angle 0.63652 (10453) hydrogen bonds : bond 0.03814 ( 503) hydrogen bonds : angle 4.54408 ( 1473) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 266 LEU cc_start: 0.9577 (tt) cc_final: 0.9223 (pp) REVERT: H 292 CYS cc_start: 0.9002 (p) cc_final: 0.8784 (p) REVERT: H 304 THR cc_start: 0.9456 (m) cc_final: 0.9210 (p) REVERT: H 374 GLN cc_start: 0.9104 (mm-40) cc_final: 0.8375 (mm-40) REVERT: H 412 MET cc_start: 0.8366 (mpp) cc_final: 0.8020 (tpp) REVERT: H 418 CYS cc_start: 0.9232 (t) cc_final: 0.8816 (p) REVERT: H 609 LYS cc_start: 0.9681 (mmtm) cc_final: 0.9303 (mmmm) REVERT: H 1140 LEU cc_start: 0.9347 (mt) cc_final: 0.9055 (mt) REVERT: H 1164 PHE cc_start: 0.8693 (t80) cc_final: 0.8300 (t80) REVERT: H 1180 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7728 (tttt) REVERT: H 1202 SER cc_start: 0.8804 (m) cc_final: 0.8450 (t) REVERT: H 1233 SER cc_start: 0.9636 (m) cc_final: 0.9322 (p) REVERT: H 1236 ILE cc_start: 0.9326 (tp) cc_final: 0.9093 (tp) REVERT: H 1247 TRP cc_start: 0.9497 (t60) cc_final: 0.9161 (t60) REVERT: H 1306 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7984 (mm-30) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.0591 time to fit residues: 13.8260 Evaluate side-chains 136 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 109 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 44 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 38 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 chunk 104 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 386 ASN ** H 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.078030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.061023 restraints weight = 32673.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.062941 restraints weight = 21559.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.064349 restraints weight = 15597.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.065427 restraints weight = 11996.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.066204 restraints weight = 9655.646| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 1.0223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7590 Z= 0.126 Angle : 0.571 8.874 10453 Z= 0.298 Chirality : 0.043 0.189 1295 Planarity : 0.004 0.081 1380 Dihedral : 4.414 40.665 1218 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.21 % Allowed : 2.11 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.09 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.26), residues: 1159 helix: 1.60 (0.20), residues: 732 sheet: -5.04 (0.79), residues: 22 loop : -2.99 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 258 TYR 0.021 0.002 TYR H 263 PHE 0.021 0.002 PHE H1177 TRP 0.012 0.001 TRP H 439 HIS 0.006 0.001 HIS H 867 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7590) covalent geometry : angle 0.57128 (10453) hydrogen bonds : bond 0.03432 ( 503) hydrogen bonds : angle 4.30785 ( 1473) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 245 ILE cc_start: 0.9107 (tt) cc_final: 0.8878 (mp) REVERT: H 292 CYS cc_start: 0.9009 (p) cc_final: 0.8768 (p) REVERT: H 304 THR cc_start: 0.9544 (m) cc_final: 0.9270 (p) REVERT: H 387 LEU cc_start: 0.8692 (mt) cc_final: 0.8401 (mt) REVERT: H 396 TYR cc_start: 0.8615 (t80) cc_final: 0.8365 (t80) REVERT: H 412 MET cc_start: 0.8369 (mpp) cc_final: 0.7982 (tpp) REVERT: H 418 CYS cc_start: 0.9649 (t) cc_final: 0.9264 (p) REVERT: H 609 LYS cc_start: 0.9677 (mmtm) cc_final: 0.9408 (mmmm) REVERT: H 1140 LEU cc_start: 0.9406 (mt) cc_final: 0.9090 (mt) REVERT: H 1179 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8595 (tp40) REVERT: H 1180 LYS cc_start: 0.8776 (ttpt) cc_final: 0.8540 (tttt) REVERT: H 1202 SER cc_start: 0.8993 (m) cc_final: 0.8669 (p) REVERT: H 1225 GLN cc_start: 0.8558 (mt0) cc_final: 0.8252 (mt0) REVERT: H 1233 SER cc_start: 0.9756 (m) cc_final: 0.9450 (p) REVERT: H 1239 LEU cc_start: 0.9357 (mm) cc_final: 0.8948 (tp) REVERT: H 1246 ARG cc_start: 0.9038 (mmp80) cc_final: 0.8418 (mmp80) REVERT: H 1290 MET cc_start: 0.8346 (mmp) cc_final: 0.8037 (mmm) REVERT: H 1293 ASN cc_start: 0.9202 (p0) cc_final: 0.8826 (p0) REVERT: H 1306 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8216 (mm-30) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.0589 time to fit residues: 13.8070 Evaluate side-chains 138 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 88 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 58 optimal weight: 50.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 374 GLN H 386 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.076994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.060477 restraints weight = 32132.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.062248 restraints weight = 21952.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.063590 restraints weight = 16199.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.064599 restraints weight = 12653.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.065405 restraints weight = 10336.055| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 1.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7590 Z= 0.126 Angle : 0.571 7.386 10453 Z= 0.295 Chirality : 0.042 0.220 1295 Planarity : 0.004 0.078 1380 Dihedral : 4.264 39.994 1218 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.21 % Allowed : 2.32 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.09 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.26), residues: 1159 helix: 1.70 (0.20), residues: 733 sheet: -4.96 (0.80), residues: 22 loop : -2.95 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 598 TYR 0.015 0.001 TYR H1064 PHE 0.019 0.002 PHE H1177 TRP 0.012 0.001 TRP H1247 HIS 0.006 0.001 HIS H 867 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7590) covalent geometry : angle 0.57092 (10453) hydrogen bonds : bond 0.03355 ( 503) hydrogen bonds : angle 4.19557 ( 1473) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 292 CYS cc_start: 0.9037 (p) cc_final: 0.8652 (p) REVERT: H 304 THR cc_start: 0.9564 (m) cc_final: 0.9289 (p) REVERT: H 325 ASP cc_start: 0.7860 (m-30) cc_final: 0.7379 (m-30) REVERT: H 396 TYR cc_start: 0.8646 (t80) cc_final: 0.8319 (t80) REVERT: H 418 CYS cc_start: 0.9625 (t) cc_final: 0.9152 (p) REVERT: H 588 THR cc_start: 0.9318 (m) cc_final: 0.9066 (p) REVERT: H 609 LYS cc_start: 0.9652 (mmtm) cc_final: 0.9329 (mmmm) REVERT: H 1179 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8745 (tp40) REVERT: H 1180 LYS cc_start: 0.8782 (ttpt) cc_final: 0.8565 (tttt) REVERT: H 1188 ASP cc_start: 0.8667 (t70) cc_final: 0.8402 (t0) REVERT: H 1192 LEU cc_start: 0.9497 (tp) cc_final: 0.9287 (tp) REVERT: H 1202 SER cc_start: 0.9055 (m) cc_final: 0.8719 (p) REVERT: H 1225 GLN cc_start: 0.8549 (mt0) cc_final: 0.8323 (mt0) REVERT: H 1233 SER cc_start: 0.9762 (m) cc_final: 0.9445 (p) REVERT: H 1239 LEU cc_start: 0.9339 (mm) cc_final: 0.8948 (tp) REVERT: H 1246 ARG cc_start: 0.9087 (mmp80) cc_final: 0.8323 (mmp80) REVERT: H 1290 MET cc_start: 0.8411 (mmp) cc_final: 0.7901 (mmp) REVERT: H 1293 ASN cc_start: 0.9128 (p0) cc_final: 0.8736 (p0) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.0657 time to fit residues: 14.5924 Evaluate side-chains 142 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 112 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 58 optimal weight: 40.0000 chunk 64 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 115 optimal weight: 0.0570 chunk 111 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.075985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.059495 restraints weight = 32570.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.061281 restraints weight = 21995.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.062676 restraints weight = 16137.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.063693 restraints weight = 12513.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.064461 restraints weight = 10153.405| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 1.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7590 Z= 0.133 Angle : 0.589 6.664 10453 Z= 0.311 Chirality : 0.043 0.185 1295 Planarity : 0.004 0.075 1380 Dihedral : 4.168 38.782 1218 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.09 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.26), residues: 1159 helix: 1.74 (0.20), residues: 736 sheet: -4.16 (0.84), residues: 28 loop : -2.87 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H1187 TYR 0.022 0.002 TYR H1181 PHE 0.029 0.002 PHE H1177 TRP 0.012 0.001 TRP H 430 HIS 0.006 0.001 HIS H 867 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7590) covalent geometry : angle 0.58888 (10453) hydrogen bonds : bond 0.03517 ( 503) hydrogen bonds : angle 4.19741 ( 1473) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 266 LEU cc_start: 0.9740 (tt) cc_final: 0.9377 (pp) REVERT: H 292 CYS cc_start: 0.9077 (p) cc_final: 0.8781 (p) REVERT: H 304 THR cc_start: 0.9620 (m) cc_final: 0.9281 (p) REVERT: H 382 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8436 (tm-30) REVERT: H 396 TYR cc_start: 0.8642 (t80) cc_final: 0.8081 (t80) REVERT: H 400 MET cc_start: 0.8760 (ttm) cc_final: 0.8436 (ttm) REVERT: H 418 CYS cc_start: 0.9436 (t) cc_final: 0.9161 (t) REVERT: H 451 LEU cc_start: 0.9166 (mt) cc_final: 0.8961 (mt) REVERT: H 473 VAL cc_start: 0.9286 (t) cc_final: 0.8872 (p) REVERT: H 583 PHE cc_start: 0.9498 (m-10) cc_final: 0.8895 (m-80) REVERT: H 588 THR cc_start: 0.9517 (m) cc_final: 0.9281 (p) REVERT: H 609 LYS cc_start: 0.9630 (mmtm) cc_final: 0.9379 (mmmm) REVERT: H 1179 GLN cc_start: 0.9121 (mm-40) cc_final: 0.8811 (tp40) REVERT: H 1180 LYS cc_start: 0.8775 (ttpt) cc_final: 0.8544 (tttt) REVERT: H 1188 ASP cc_start: 0.8809 (t70) cc_final: 0.8547 (t0) REVERT: H 1202 SER cc_start: 0.9228 (m) cc_final: 0.8885 (p) REVERT: H 1207 THR cc_start: 0.8198 (p) cc_final: 0.7070 (p) REVERT: H 1215 ARG cc_start: 0.8970 (mtm110) cc_final: 0.8584 (mtm110) REVERT: H 1225 GLN cc_start: 0.8647 (mt0) cc_final: 0.8401 (mt0) REVERT: H 1233 SER cc_start: 0.9800 (m) cc_final: 0.9463 (p) REVERT: H 1246 ARG cc_start: 0.8983 (mmp80) cc_final: 0.8641 (mmp80) REVERT: H 1306 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8364 (mm-30) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.0650 time to fit residues: 14.8361 Evaluate side-chains 140 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 62 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 0.0670 chunk 39 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.077032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.060669 restraints weight = 31981.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.062451 restraints weight = 21852.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.063800 restraints weight = 16147.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.064832 restraints weight = 12579.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.065452 restraints weight = 10234.998| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 1.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 7590 Z= 0.116 Angle : 0.585 7.638 10453 Z= 0.299 Chirality : 0.042 0.161 1295 Planarity : 0.004 0.074 1380 Dihedral : 4.043 37.566 1218 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.09 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.26), residues: 1159 helix: 1.72 (0.20), residues: 735 sheet: -4.06 (0.90), residues: 27 loop : -2.82 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 598 TYR 0.018 0.001 TYR H1181 PHE 0.019 0.002 PHE H 545 TRP 0.010 0.001 TRP H 430 HIS 0.006 0.001 HIS H 867 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7590) covalent geometry : angle 0.58459 (10453) hydrogen bonds : bond 0.03231 ( 503) hydrogen bonds : angle 4.13707 ( 1473) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 266 LEU cc_start: 0.9745 (tt) cc_final: 0.9417 (pp) REVERT: H 292 CYS cc_start: 0.9057 (p) cc_final: 0.8739 (p) REVERT: H 300 ILE cc_start: 0.9405 (pt) cc_final: 0.9195 (pt) REVERT: H 304 THR cc_start: 0.9619 (m) cc_final: 0.9348 (p) REVERT: H 325 ASP cc_start: 0.8031 (m-30) cc_final: 0.7643 (m-30) REVERT: H 385 ILE cc_start: 0.9486 (mt) cc_final: 0.9217 (tt) REVERT: H 396 TYR cc_start: 0.9034 (t80) cc_final: 0.8520 (t80) REVERT: H 400 MET cc_start: 0.8673 (ttm) cc_final: 0.8338 (ttm) REVERT: H 418 CYS cc_start: 0.9406 (t) cc_final: 0.9108 (t) REVERT: H 451 LEU cc_start: 0.9151 (mt) cc_final: 0.8945 (mt) REVERT: H 473 VAL cc_start: 0.9298 (t) cc_final: 0.8910 (p) REVERT: H 583 PHE cc_start: 0.9481 (m-10) cc_final: 0.8775 (m-80) REVERT: H 588 THR cc_start: 0.9482 (m) cc_final: 0.9275 (p) REVERT: H 598 ARG cc_start: 0.9122 (mmp80) cc_final: 0.8822 (mmp80) REVERT: H 609 LYS cc_start: 0.9532 (mmtm) cc_final: 0.9212 (mmmm) REVERT: H 1179 GLN cc_start: 0.9148 (mm-40) cc_final: 0.8824 (tp40) REVERT: H 1188 ASP cc_start: 0.8806 (t70) cc_final: 0.8540 (t0) REVERT: H 1192 LEU cc_start: 0.9531 (tp) cc_final: 0.9326 (tp) REVERT: H 1202 SER cc_start: 0.9166 (m) cc_final: 0.8827 (p) REVERT: H 1207 THR cc_start: 0.8208 (p) cc_final: 0.7046 (p) REVERT: H 1215 ARG cc_start: 0.8856 (mtm110) cc_final: 0.8489 (mtm110) REVERT: H 1225 GLN cc_start: 0.8628 (mt0) cc_final: 0.8422 (mm-40) REVERT: H 1233 SER cc_start: 0.9784 (m) cc_final: 0.9446 (p) REVERT: H 1235 ASN cc_start: 0.9734 (m-40) cc_final: 0.9359 (m110) REVERT: H 1239 LEU cc_start: 0.9495 (mm) cc_final: 0.9101 (tp) REVERT: H 1246 ARG cc_start: 0.9006 (mmp80) cc_final: 0.8165 (mmp80) REVERT: H 1306 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8462 (mm-30) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.0607 time to fit residues: 14.6854 Evaluate side-chains 146 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 37 optimal weight: 0.0570 chunk 53 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 29 optimal weight: 0.0970 chunk 108 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 115 optimal weight: 20.0000 overall best weight: 1.3300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.076824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.059687 restraints weight = 34044.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.061596 restraints weight = 22819.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.062988 restraints weight = 16635.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.064063 restraints weight = 12857.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.064845 restraints weight = 10405.480| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 1.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7590 Z= 0.141 Angle : 0.605 7.465 10453 Z= 0.313 Chirality : 0.044 0.210 1295 Planarity : 0.004 0.068 1380 Dihedral : 4.081 36.471 1218 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.09 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.26), residues: 1159 helix: 1.73 (0.20), residues: 735 sheet: -4.14 (0.87), residues: 27 loop : -2.68 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 306 TYR 0.017 0.002 TYR H1181 PHE 0.024 0.002 PHE H 432 TRP 0.014 0.001 TRP H 430 HIS 0.005 0.001 HIS H 867 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7590) covalent geometry : angle 0.60485 (10453) hydrogen bonds : bond 0.03410 ( 503) hydrogen bonds : angle 4.25056 ( 1473) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 266 LEU cc_start: 0.9733 (tt) cc_final: 0.9486 (pp) REVERT: H 292 CYS cc_start: 0.9011 (p) cc_final: 0.8745 (p) REVERT: H 300 ILE cc_start: 0.9339 (pt) cc_final: 0.9114 (pt) REVERT: H 308 LEU cc_start: 0.9369 (mm) cc_final: 0.9078 (pp) REVERT: H 325 ASP cc_start: 0.8448 (m-30) cc_final: 0.8030 (m-30) REVERT: H 412 MET cc_start: 0.8174 (tpt) cc_final: 0.7624 (mpp) REVERT: H 418 CYS cc_start: 0.9417 (t) cc_final: 0.9100 (t) REVERT: H 473 VAL cc_start: 0.9450 (t) cc_final: 0.9037 (p) REVERT: H 580 LEU cc_start: 0.9558 (tp) cc_final: 0.9345 (tp) REVERT: H 609 LYS cc_start: 0.9480 (mmtm) cc_final: 0.9260 (mmmm) REVERT: H 612 GLU cc_start: 0.9193 (mp0) cc_final: 0.8923 (mp0) REVERT: H 1146 SER cc_start: 0.9507 (m) cc_final: 0.9157 (p) REVERT: H 1179 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8912 (tp40) REVERT: H 1188 ASP cc_start: 0.8870 (t70) cc_final: 0.8629 (t0) REVERT: H 1202 SER cc_start: 0.9409 (m) cc_final: 0.9147 (p) REVERT: H 1215 ARG cc_start: 0.8844 (mtm110) cc_final: 0.8451 (mtm110) REVERT: H 1225 GLN cc_start: 0.8717 (mt0) cc_final: 0.8256 (mt0) REVERT: H 1226 LYS cc_start: 0.8401 (mttt) cc_final: 0.8059 (tptp) REVERT: H 1229 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8077 (mt-10) REVERT: H 1233 SER cc_start: 0.9814 (m) cc_final: 0.9473 (p) REVERT: H 1246 ARG cc_start: 0.8896 (mmp80) cc_final: 0.8336 (mmp80) REVERT: H 1253 GLU cc_start: 0.8710 (pm20) cc_final: 0.8379 (pm20) REVERT: H 1306 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8666 (mm-30) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.0603 time to fit residues: 14.3385 Evaluate side-chains 148 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 81 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 78 optimal weight: 0.1980 chunk 110 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.078523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.061101 restraints weight = 33412.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.063048 restraints weight = 22407.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.064452 restraints weight = 16310.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.065570 restraints weight = 12625.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066420 restraints weight = 10198.753| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 1.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 7590 Z= 0.114 Angle : 0.585 8.109 10453 Z= 0.298 Chirality : 0.042 0.165 1295 Planarity : 0.004 0.068 1380 Dihedral : 3.953 35.460 1218 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.09 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.26), residues: 1159 helix: 1.77 (0.20), residues: 739 sheet: -4.02 (0.89), residues: 27 loop : -2.64 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 306 TYR 0.017 0.002 TYR H1287 PHE 0.027 0.002 PHE H 305 TRP 0.010 0.001 TRP H 430 HIS 0.005 0.001 HIS H 867 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7590) covalent geometry : angle 0.58473 (10453) hydrogen bonds : bond 0.03283 ( 503) hydrogen bonds : angle 4.18400 ( 1473) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1058.88 seconds wall clock time: 18 minutes 54.44 seconds (1134.44 seconds total)