Starting phenix.real_space_refine on Mon Mar 11 07:20:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzc_20534/03_2024/6pzc_20534_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzc_20534/03_2024/6pzc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzc_20534/03_2024/6pzc_20534.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzc_20534/03_2024/6pzc_20534.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzc_20534/03_2024/6pzc_20534_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzc_20534/03_2024/6pzc_20534_neut.pdb" } resolution = 4.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Residue "H ARG 289": "NH1" <-> "NH2" Residue "H ARG 298": "NH1" <-> "NH2" Residue "H ARG 306": "NH1" <-> "NH2" Residue "H ARG 598": "NH1" <-> "NH2" Residue "H ARG 702": "NH1" <-> "NH2" Residue "H ARG 1300": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: {'GLN:plan1': 33, 'HIS:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 20, 'TRP:plan': 3, 'ASP:plan': 35, 'PHE:plan': 21, 'GLU:plan': 36, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 807 Time building chain proxies: 4.77, per 1000 atoms: 0.64 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 - 3.50 Amino acid : False - 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: 3.23 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 0.85 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: 2.81 Time building geometry restraints manager: 3.49 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: 97.32 - 104.65: 106 104.65 - 111.98: 3809 111.98 - 119.32: 2439 119.32 - 126.65: 4004 126.65 - 133.99: 95 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 2.520 nonbonded pdb=" N ASN H 781 " pdb=" OE2 GLU H1206 " model vdw 2.154 2.520 nonbonded pdb=" O LEU H1192 " pdb=" OG1 THR H1196 " model vdw 2.211 2.440 nonbonded pdb=" O LEU H 367 " pdb=" OG1 THR H 371 " model vdw 2.234 2.440 nonbonded pdb=" O LEU H1148 " pdb=" OG SER H1152 " model vdw 2.247 2.440 ... (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: 0.270 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: 1.300 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 25.360 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.350 ------------------------------------------------------------------------------- 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= 0.540 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 : 7.52 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.15 (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 TRP 0.062 0.005 TRP H 232 HIS 0.010 0.004 HIS H 584 PHE 0.033 0.004 PHE H 270 TYR 0.043 0.004 TYR H 475 ARG 0.013 0.002 ARG H 370 *********************** 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 fitting. rotamer outliers: 2 poor density : 160 time to evaluate : 0.860 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: 0.7240 (t80) REVERT: H 367 LEU cc_start: 0.8209 (mt) cc_final: 0.7866 (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: 0.7322 (mp) REVERT: H 1214 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7121 (mp) outliers start: 2 outliers final: 0 residues processed: 161 average time/residue: 0.1964 time to fit residues: 41.7571 Evaluate side-chains 108 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 20.0000 chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 59 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 234 ASN ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.5813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 7590 Z= 0.370 Angle : 0.817 10.848 10453 Z= 0.443 Chirality : 0.046 0.199 1295 Planarity : 0.007 0.096 1380 Dihedral : 6.088 45.006 1218 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.23), residues: 1159 helix: -0.68 (0.18), residues: 746 sheet: -4.95 (0.59), residues: 21 loop : -3.87 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.004 TRP H 430 HIS 0.010 0.002 HIS H 867 PHE 0.036 0.003 PHE H 270 TYR 0.028 0.003 TYR H1254 ARG 0.011 0.002 ARG H 598 *********************** 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 172 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 167 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 264 GLN cc_start: 0.8570 (tp-100) cc_final: 0.8210 (tp-100) REVERT: H 268 VAL cc_start: 0.9126 (t) cc_final: 0.8484 (t) REVERT: H 363 PHE cc_start: 0.7215 (t80) cc_final: 0.6885 (t80) REVERT: H 367 LEU cc_start: 0.9406 (mt) cc_final: 0.9030 (mt) REVERT: H 418 CYS cc_start: 0.8697 (t) cc_final: 0.8350 (p) REVERT: H 421 VAL cc_start: 0.8512 (t) cc_final: 0.8072 (m) REVERT: H 444 GLN cc_start: 0.8972 (mt0) cc_final: 0.8691 (tp-100) REVERT: H 445 ILE cc_start: 0.9361 (mt) cc_final: 0.9130 (mm) REVERT: H 602 LYS cc_start: 0.8886 (mmtm) cc_final: 0.8473 (mmtm) REVERT: H 1068 PHE cc_start: 0.4185 (t80) cc_final: 0.3795 (t80) REVERT: H 1139 THR cc_start: 0.8346 (m) cc_final: 0.7721 (t) REVERT: H 1140 LEU cc_start: 0.9153 (mt) cc_final: 0.8942 (mt) REVERT: H 1202 SER cc_start: 0.8675 (m) cc_final: 0.8044 (t) REVERT: H 1209 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7086 (tt0) REVERT: H 1223 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7438 (m-10) outliers start: 5 outliers final: 1 residues processed: 171 average time/residue: 0.1617 time to fit residues: 38.7350 Evaluate side-chains 131 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 114 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 105 optimal weight: 0.0000 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.6576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7590 Z= 0.169 Angle : 0.586 8.605 10453 Z= 0.311 Chirality : 0.042 0.158 1295 Planarity : 0.005 0.092 1380 Dihedral : 5.201 43.945 1218 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.24), residues: 1159 helix: 0.46 (0.19), residues: 746 sheet: -4.46 (0.73), residues: 21 loop : -3.71 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP H 430 HIS 0.008 0.001 HIS H 867 PHE 0.018 0.002 PHE H 270 TYR 0.031 0.002 TYR H1219 ARG 0.017 0.001 ARG H 486 *********************** 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 154 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 237 ILE cc_start: 0.8212 (pt) cc_final: 0.7940 (pt) REVERT: H 264 GLN cc_start: 0.8533 (tp-100) cc_final: 0.8142 (tp-100) REVERT: H 268 VAL cc_start: 0.9104 (t) cc_final: 0.8473 (t) REVERT: H 314 PHE cc_start: 0.6442 (m-80) cc_final: 0.4354 (m-80) REVERT: H 363 PHE cc_start: 0.7106 (t80) cc_final: 0.6784 (t80) REVERT: H 367 LEU cc_start: 0.9389 (mt) cc_final: 0.8952 (mt) REVERT: H 445 ILE cc_start: 0.9124 (mt) cc_final: 0.8797 (mm) REVERT: H 580 LEU cc_start: 0.8431 (tp) cc_final: 0.8211 (tp) REVERT: H 602 LYS cc_start: 0.8992 (mmtm) cc_final: 0.8556 (mmtm) REVERT: H 1139 THR cc_start: 0.8222 (m) cc_final: 0.7726 (t) REVERT: H 1140 LEU cc_start: 0.9132 (mt) cc_final: 0.8893 (mt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1488 time to fit residues: 33.1905 Evaluate side-chains 124 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 71 optimal weight: 0.0670 chunk 106 optimal weight: 4.9990 chunk 113 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 overall best weight: 3.1924 ------------------------------------------------------------------------------- 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 817 HIS ** H1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 1.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 7590 Z= 0.391 Angle : 0.850 10.039 10453 Z= 0.449 Chirality : 0.047 0.203 1295 Planarity : 0.006 0.080 1380 Dihedral : 5.856 40.436 1218 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.54 % Favored : 91.29 % Rotamer: Outliers : 0.84 % Allowed : 8.65 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.09 % Twisted Proline : 2.70 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.24), residues: 1159 helix: 0.21 (0.19), residues: 726 sheet: -4.62 (0.59), residues: 31 loop : -3.44 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP H 232 HIS 0.009 0.003 HIS H1203 PHE 0.029 0.004 PHE H 295 TYR 0.037 0.004 TYR H1254 ARG 0.006 0.001 ARG H 298 *********************** 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 179 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 175 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 237 ILE cc_start: 0.9154 (pt) cc_final: 0.8590 (pt) REVERT: H 260 LEU cc_start: 0.9266 (tt) cc_final: 0.8981 (tp) REVERT: H 314 PHE cc_start: 0.7749 (m-80) cc_final: 0.7327 (m-10) REVERT: H 367 LEU cc_start: 0.9278 (mt) cc_final: 0.9043 (mt) REVERT: H 393 THR cc_start: 0.9161 (m) cc_final: 0.8954 (m) REVERT: H 444 GLN cc_start: 0.8903 (tp-100) cc_final: 0.8569 (tp40) REVERT: H 580 LEU cc_start: 0.9046 (tp) cc_final: 0.8798 (tp) REVERT: H 1143 LEU cc_start: 0.9668 (tp) cc_final: 0.9427 (tt) REVERT: H 1146 SER cc_start: 0.9184 (m) cc_final: 0.8743 (p) REVERT: H 1147 THR cc_start: 0.9010 (m) cc_final: 0.8793 (p) REVERT: H 1202 SER cc_start: 0.9312 (m) cc_final: 0.8998 (p) REVERT: H 1225 GLN cc_start: 0.8126 (pt0) cc_final: 0.7793 (pt0) REVERT: H 1233 SER cc_start: 0.9784 (m) cc_final: 0.9475 (p) REVERT: H 1239 LEU cc_start: 0.9545 (mt) cc_final: 0.9086 (tt) REVERT: H 1247 TRP cc_start: 0.8643 (t60) cc_final: 0.8198 (t60) REVERT: H 1249 GLU cc_start: 0.8164 (pp20) cc_final: 0.7858 (pp20) REVERT: H 1290 MET cc_start: 0.8360 (mmp) cc_final: 0.8122 (mmm) outliers start: 4 outliers final: 0 residues processed: 178 average time/residue: 0.1540 time to fit residues: 38.8729 Evaluate side-chains 140 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 7.9990 chunk 1 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 78 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 386 ASN H1179 GLN ** H1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 1.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7590 Z= 0.260 Angle : 0.648 9.445 10453 Z= 0.345 Chirality : 0.043 0.186 1295 Planarity : 0.005 0.080 1380 Dihedral : 5.146 39.649 1218 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.21 % Allowed : 3.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.25), residues: 1159 helix: 0.74 (0.19), residues: 731 sheet: -4.58 (0.62), residues: 31 loop : -3.21 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 232 HIS 0.007 0.001 HIS H 867 PHE 0.033 0.002 PHE H 295 TYR 0.017 0.002 TYR H 475 ARG 0.005 0.001 ARG H 388 *********************** 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 172 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 292 CYS cc_start: 0.8305 (p) cc_final: 0.8093 (p) REVERT: H 367 LEU cc_start: 0.9366 (mt) cc_final: 0.9119 (mt) REVERT: H 385 ILE cc_start: 0.9176 (mt) cc_final: 0.8937 (mt) REVERT: H 480 LYS cc_start: 0.9485 (mmtt) cc_final: 0.9130 (mmmt) REVERT: H 583 PHE cc_start: 0.9040 (m-10) cc_final: 0.8359 (m-80) REVERT: H 1142 CYS cc_start: 0.8427 (m) cc_final: 0.7824 (t) REVERT: H 1143 LEU cc_start: 0.9686 (tp) cc_final: 0.9473 (tt) REVERT: H 1146 SER cc_start: 0.9271 (m) cc_final: 0.9034 (p) REVERT: H 1202 SER cc_start: 0.9316 (m) cc_final: 0.9084 (p) REVERT: H 1233 SER cc_start: 0.9761 (m) cc_final: 0.9515 (p) REVERT: H 1239 LEU cc_start: 0.9487 (mt) cc_final: 0.9213 (tt) REVERT: H 1246 ARG cc_start: 0.9054 (mmp80) cc_final: 0.8699 (mmp80) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.1842 time to fit residues: 44.7498 Evaluate side-chains 140 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 66 optimal weight: 0.0470 chunk 27 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 93 optimal weight: 0.0060 chunk 52 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 30.0000 chunk 109 optimal weight: 10.0000 overall best weight: 2.1696 ------------------------------------------------------------------------------- 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** ** H1225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 1.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7590 Z= 0.247 Angle : 0.649 9.135 10453 Z= 0.346 Chirality : 0.044 0.219 1295 Planarity : 0.005 0.075 1380 Dihedral : 4.912 39.365 1218 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.09 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.25), residues: 1159 helix: 0.95 (0.20), residues: 731 sheet: -4.57 (0.63), residues: 31 loop : -3.08 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP H 232 HIS 0.006 0.001 HIS H 867 PHE 0.028 0.002 PHE H1177 TYR 0.021 0.002 TYR H1294 ARG 0.006 0.001 ARG H 258 *********************** 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 171 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 292 CYS cc_start: 0.8236 (p) cc_final: 0.7982 (p) REVERT: H 367 LEU cc_start: 0.9374 (mt) cc_final: 0.8910 (mt) REVERT: H 385 ILE cc_start: 0.9115 (mt) cc_final: 0.8881 (mt) REVERT: H 420 LEU cc_start: 0.9096 (tt) cc_final: 0.8547 (tt) REVERT: H 580 LEU cc_start: 0.8794 (tp) cc_final: 0.8590 (tp) REVERT: H 1142 CYS cc_start: 0.8540 (m) cc_final: 0.7982 (t) REVERT: H 1143 LEU cc_start: 0.9736 (tp) cc_final: 0.9498 (tt) REVERT: H 1146 SER cc_start: 0.9246 (m) cc_final: 0.9044 (p) REVERT: H 1206 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7585 (tp30) REVERT: H 1215 ARG cc_start: 0.8411 (mtm110) cc_final: 0.7980 (mtm110) REVERT: H 1233 SER cc_start: 0.9781 (m) cc_final: 0.9506 (p) REVERT: H 1234 ASN cc_start: 0.8803 (t0) cc_final: 0.8213 (t0) REVERT: H 1238 SER cc_start: 0.8384 (m) cc_final: 0.7951 (p) REVERT: H 1239 LEU cc_start: 0.9462 (mt) cc_final: 0.9084 (tt) REVERT: H 1246 ARG cc_start: 0.8776 (mmp80) cc_final: 0.8567 (mmp80) REVERT: H 1290 MET cc_start: 0.8490 (mmp) cc_final: 0.7823 (mmp) REVERT: H 1293 ASN cc_start: 0.8503 (p0) cc_final: 0.8289 (t0) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1603 time to fit residues: 39.7548 Evaluate side-chains 146 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 95 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN ** H1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 1.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7590 Z= 0.253 Angle : 0.654 11.685 10453 Z= 0.346 Chirality : 0.044 0.173 1295 Planarity : 0.005 0.075 1380 Dihedral : 4.805 37.439 1218 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.09 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1159 helix: 1.06 (0.19), residues: 733 sheet: -4.49 (0.64), residues: 31 loop : -3.06 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP H 232 HIS 0.006 0.001 HIS H 867 PHE 0.017 0.002 PHE H 433 TYR 0.017 0.002 TYR H 378 ARG 0.005 0.001 ARG H1222 *********************** 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 170 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 264 GLN cc_start: 0.8934 (pm20) cc_final: 0.8622 (pm20) REVERT: H 367 LEU cc_start: 0.9291 (mt) cc_final: 0.8893 (mt) REVERT: H 385 ILE cc_start: 0.9270 (mt) cc_final: 0.8814 (tt) REVERT: H 388 ARG cc_start: 0.7740 (ttm110) cc_final: 0.6689 (ttp-170) REVERT: H 420 LEU cc_start: 0.9178 (tt) cc_final: 0.8305 (mt) REVERT: H 429 MET cc_start: 0.7452 (tpp) cc_final: 0.7244 (tpp) REVERT: H 545 PHE cc_start: 0.8277 (t80) cc_final: 0.7768 (t80) REVERT: H 1142 CYS cc_start: 0.8528 (m) cc_final: 0.8121 (t) REVERT: H 1143 LEU cc_start: 0.9735 (tp) cc_final: 0.9477 (tt) REVERT: H 1215 ARG cc_start: 0.8175 (mtm110) cc_final: 0.7923 (mtm110) REVERT: H 1233 SER cc_start: 0.9769 (m) cc_final: 0.9521 (p) REVERT: H 1234 ASN cc_start: 0.8439 (t0) cc_final: 0.6985 (t0) REVERT: H 1239 LEU cc_start: 0.9433 (mt) cc_final: 0.9158 (tt) REVERT: H 1246 ARG cc_start: 0.8811 (mmp80) cc_final: 0.8551 (mmp80) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1632 time to fit residues: 39.4672 Evaluate side-chains 143 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN H 426 ASN H1203 HIS ** H1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 1.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7590 Z= 0.182 Angle : 0.612 9.275 10453 Z= 0.316 Chirality : 0.043 0.201 1295 Planarity : 0.004 0.073 1380 Dihedral : 4.593 37.660 1218 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.09 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 1159 helix: 1.41 (0.20), residues: 734 sheet: -4.33 (0.64), residues: 31 loop : -2.92 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 232 HIS 0.007 0.001 HIS H 867 PHE 0.016 0.002 PHE H1177 TYR 0.030 0.002 TYR H1294 ARG 0.003 0.000 ARG H 598 *********************** 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 170 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 264 GLN cc_start: 0.9012 (pm20) cc_final: 0.8635 (pm20) REVERT: H 292 CYS cc_start: 0.8048 (p) cc_final: 0.7734 (t) REVERT: H 426 ASN cc_start: 0.9249 (m-40) cc_final: 0.9017 (m110) REVERT: H 429 MET cc_start: 0.7612 (tpp) cc_final: 0.7103 (tpp) REVERT: H 1215 ARG cc_start: 0.8173 (mtm110) cc_final: 0.7888 (mtm110) REVERT: H 1226 LYS cc_start: 0.8753 (tmtt) cc_final: 0.7885 (tptp) REVERT: H 1233 SER cc_start: 0.9758 (m) cc_final: 0.9531 (p) REVERT: H 1234 ASN cc_start: 0.8873 (t0) cc_final: 0.8178 (t0) REVERT: H 1239 LEU cc_start: 0.9415 (mt) cc_final: 0.9152 (tt) REVERT: H 1246 ARG cc_start: 0.8804 (mmp80) cc_final: 0.8463 (mmp80) REVERT: H 1255 ILE cc_start: 0.8859 (mp) cc_final: 0.8631 (mp) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1566 time to fit residues: 37.4696 Evaluate side-chains 142 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.0570 chunk 105 optimal weight: 4.9990 chunk 108 optimal weight: 0.1980 chunk 63 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 0.0060 chunk 69 optimal weight: 7.9990 overall best weight: 0.8518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 262 ASN ** H 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN ** H1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 1.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 7590 Z= 0.167 Angle : 0.611 9.279 10453 Z= 0.312 Chirality : 0.043 0.206 1295 Planarity : 0.004 0.070 1380 Dihedral : 4.415 36.298 1218 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.26 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.09 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1159 helix: 1.59 (0.20), residues: 736 sheet: -4.04 (0.71), residues: 31 loop : -2.84 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 232 HIS 0.006 0.001 HIS H 867 PHE 0.015 0.002 PHE H1177 TYR 0.017 0.002 TYR H 377 ARG 0.003 0.000 ARG H 265 *********************** 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 164 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 264 GLN cc_start: 0.9029 (pm20) cc_final: 0.8606 (pm20) REVERT: H 292 CYS cc_start: 0.7984 (p) cc_final: 0.7741 (t) REVERT: H 354 ASN cc_start: 0.6430 (t0) cc_final: 0.6083 (t0) REVERT: H 357 VAL cc_start: 0.8332 (t) cc_final: 0.8100 (t) REVERT: H 426 ASN cc_start: 0.9075 (m-40) cc_final: 0.8800 (m110) REVERT: H 429 MET cc_start: 0.7494 (tpp) cc_final: 0.7098 (tpp) REVERT: H 1140 LEU cc_start: 0.9331 (tt) cc_final: 0.9066 (pp) REVERT: H 1215 ARG cc_start: 0.8044 (mtm110) cc_final: 0.7716 (mtm110) REVERT: H 1226 LYS cc_start: 0.8587 (tmtt) cc_final: 0.8291 (tptp) REVERT: H 1233 SER cc_start: 0.9727 (m) cc_final: 0.9475 (p) REVERT: H 1246 ARG cc_start: 0.8803 (mmp80) cc_final: 0.8472 (mmp80) REVERT: H 1255 ILE cc_start: 0.8824 (mp) cc_final: 0.8535 (mp) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1590 time to fit residues: 36.5760 Evaluate side-chains 140 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 77 optimal weight: 0.4980 chunk 116 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 92 optimal weight: 30.0000 chunk 9 optimal weight: 0.2980 chunk 71 optimal weight: 0.2980 chunk 56 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN ** H1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 1.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7590 Z= 0.169 Angle : 0.623 8.622 10453 Z= 0.318 Chirality : 0.043 0.189 1295 Planarity : 0.004 0.068 1380 Dihedral : 4.343 36.264 1218 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.69 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.09 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 1159 helix: 1.63 (0.20), residues: 740 sheet: -3.43 (0.74), residues: 38 loop : -2.84 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H1037 HIS 0.006 0.001 HIS H 867 PHE 0.014 0.001 PHE H 433 TYR 0.015 0.001 TYR H 377 ARG 0.008 0.000 ARG H1145 ********************** 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 161 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 264 GLN cc_start: 0.8891 (pm20) cc_final: 0.8501 (pm20) REVERT: H 426 ASN cc_start: 0.9169 (m-40) cc_final: 0.8817 (m110) REVERT: H 429 MET cc_start: 0.7694 (tpp) cc_final: 0.7347 (tpp) REVERT: H 1206 GLU cc_start: 0.8244 (tt0) cc_final: 0.7473 (tp30) REVERT: H 1215 ARG cc_start: 0.8037 (mtm110) cc_final: 0.7745 (mtm110) REVERT: H 1220 GLU cc_start: 0.6880 (mp0) cc_final: 0.6543 (mp0) REVERT: H 1226 LYS cc_start: 0.8614 (tmtt) cc_final: 0.8307 (tptp) REVERT: H 1233 SER cc_start: 0.9768 (m) cc_final: 0.9503 (p) REVERT: H 1246 ARG cc_start: 0.8737 (mmp80) cc_final: 0.8268 (mmp80) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1487 time to fit residues: 34.5315 Evaluate side-chains 138 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 92 optimal weight: 30.0000 chunk 38 optimal weight: 20.0000 chunk 95 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN ** H1179 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 = 0.3407 r_free = 0.3407 target = 0.074508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.057265 restraints weight = 34951.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.058966 restraints weight = 23160.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.060039 restraints weight = 16830.540| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 1.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7590 Z= 0.235 Angle : 0.661 9.913 10453 Z= 0.346 Chirality : 0.045 0.203 1295 Planarity : 0.005 0.063 1380 Dihedral : 4.571 34.615 1218 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.82 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.09 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.26), residues: 1159 helix: 1.44 (0.20), residues: 740 sheet: -3.66 (0.69), residues: 38 loop : -2.79 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP H 232 HIS 0.006 0.001 HIS H 867 PHE 0.017 0.002 PHE H1223 TYR 0.019 0.002 TYR H 378 ARG 0.008 0.001 ARG H1145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1597.95 seconds wall clock time: 29 minutes 31.29 seconds (1771.29 seconds total)