Starting phenix.real_space_refine on Thu Jun 26 05:56:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g99_29862/06_2025/8g99_29862.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g99_29862/06_2025/8g99_29862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g99_29862/06_2025/8g99_29862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g99_29862/06_2025/8g99_29862.map" model { file = "/net/cci-nas-00/data/ceres_data/8g99_29862/06_2025/8g99_29862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g99_29862/06_2025/8g99_29862.cif" } resolution = 2.8 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= 0.001 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 2 6.06 5 S 80 5.16 5 C 9632 2.51 5 N 2568 2.21 5 O 2810 1.98 5 H 15109 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30205 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 17195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 17195 Classifications: {'peptide': 1063} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1009} Chain breaks: 3 Chain: "B" Number of atoms: 6745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 6745 Classifications: {'peptide': 431} Modifications used: {'COO': 1} Link IDs: {'PCIS': 5, 'PTRANS': 23, 'TRANS': 402} Chain breaks: 2 Chain: "C" Number of atoms: 6255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6255 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 15, 'TRANS': 365} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14369 SG CYS A1280 61.468 53.386 117.661 1.00 79.92 S ATOM 14415 SG CYS A1283 58.004 52.749 118.900 1.00 63.51 S ATOM 14770 SG CYS A1307 58.918 56.142 117.827 1.00 75.11 S ATOM 14842 SG CYS A1312 60.267 54.680 121.000 1.00 90.91 S ATOM 15411 SG CYS A1345 42.636 50.434 76.427 1.00 46.61 S ATOM 15487 SG CYS A1350 40.531 47.429 77.023 1.00 35.85 S ATOM 15786 SG CYS A1368 43.653 47.186 75.020 1.00 43.02 S ATOM 15823 SG CYS A1371 40.786 48.840 73.555 1.00 49.39 S ATOM 28797 SG CYS C 373 46.920 89.519 84.624 1.00 43.99 S ATOM 29045 SG CYS C 390 42.417 91.334 80.057 1.00 32.03 S ATOM 29697 SG CYS C 430 44.610 95.246 84.714 1.00 45.22 S ATOM 27455 SG CYS C 293 40.525 90.220 85.914 1.00 42.93 S Time building chain proxies: 13.01, per 1000 atoms: 0.43 Number of scatterers: 30205 At special positions: 0 Unit cell: (109.88, 120.54, 133.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Fe 4 26.01 S 80 16.00 O 2810 8.00 N 2568 7.00 C 9632 6.00 H 15109 1.00 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: 6.82 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 601 " pdb="FE1 SF4 C 601 " - pdb=" SG CYS C 373 " pdb="FE2 SF4 C 601 " - pdb=" SG CYS C 390 " pdb="FE4 SF4 C 601 " - pdb=" SG CYS C 293 " pdb="FE3 SF4 C 601 " - pdb=" SG CYS C 430 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1500 " pdb="ZN ZN A1500 " - pdb=" SG CYS A1283 " pdb="ZN ZN A1500 " - pdb=" SG CYS A1312 " pdb="ZN ZN A1500 " - pdb=" SG CYS A1307 " pdb="ZN ZN A1500 " - pdb=" SG CYS A1280 " pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1371 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1368 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1350 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1345 " Number of angles added : 12 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 17 sheets defined 47.5% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 409 through 420 Processing helix chain 'A' and resid 420 through 425 Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 614 through 630 Processing helix chain 'A' and resid 642 through 655 Processing helix chain 'A' and resid 658 through 663 Processing helix chain 'A' and resid 679 through 683 removed outlier: 3.667A pdb=" N ASN A 683 " --> pdb=" O ALA A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 701 Processing helix chain 'A' and resid 707 through 716 Processing helix chain 'A' and resid 724 through 729 removed outlier: 3.977A pdb=" N ARG A 729 " --> pdb=" O PRO A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 733 removed outlier: 3.531A pdb=" N ASN A 733 " --> pdb=" O ASN A 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 730 through 733' Processing helix chain 'A' and resid 734 through 760 Processing helix chain 'A' and resid 760 through 773 Processing helix chain 'A' and resid 775 through 782 removed outlier: 3.516A pdb=" N GLY A 782 " --> pdb=" O ARG A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 798 removed outlier: 4.005A pdb=" N LEU A 791 " --> pdb=" O ARG A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 871 Processing helix chain 'A' and resid 905 through 927 removed outlier: 3.585A pdb=" N GLN A 927 " --> pdb=" O GLN A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 952 Processing helix chain 'A' and resid 953 through 958 Processing helix chain 'A' and resid 965 through 990 Processing helix chain 'A' and resid 1010 through 1029 removed outlier: 3.741A pdb=" N SER A1028 " --> pdb=" O GLU A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1096 Processing helix chain 'A' and resid 1100 through 1122 Processing helix chain 'A' and resid 1125 through 1130 Processing helix chain 'A' and resid 1138 through 1142 Processing helix chain 'A' and resid 1144 through 1147 Processing helix chain 'A' and resid 1148 through 1161 removed outlier: 3.706A pdb=" N GLY A1161 " --> pdb=" O ILE A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1198 removed outlier: 4.289A pdb=" N GLU A1198 " --> pdb=" O LEU A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1210 Processing helix chain 'A' and resid 1211 through 1221 removed outlier: 3.877A pdb=" N VAL A1215 " --> pdb=" O GLN A1211 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE A1219 " --> pdb=" O VAL A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1236 Processing helix chain 'A' and resid 1238 through 1242 Processing helix chain 'A' and resid 1252 through 1258 Processing helix chain 'A' and resid 1259 through 1264 removed outlier: 4.753A pdb=" N SER A1262 " --> pdb=" O GLY A1259 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A1264 " --> pdb=" O PRO A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1270 Processing helix chain 'A' and resid 1296 through 1300 Processing helix chain 'A' and resid 1304 through 1306 No H-bonds generated for 'chain 'A' and resid 1304 through 1306' Processing helix chain 'A' and resid 1315 through 1318 Processing helix chain 'A' and resid 1319 through 1340 Processing helix chain 'A' and resid 1381 through 1395 Processing helix chain 'A' and resid 1397 through 1404 Processing helix chain 'A' and resid 1407 through 1415 Processing helix chain 'A' and resid 1419 through 1439 removed outlier: 3.548A pdb=" N THR A1432 " --> pdb=" O LYS A1428 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A1433 " --> pdb=" O LEU A1429 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A1439 " --> pdb=" O GLN A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1451 Processing helix chain 'B' and resid 212 through 236 Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 331 through 335 removed outlier: 3.816A pdb=" N PHE B 334 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 371 Processing helix chain 'B' and resid 386 through 391 Processing helix chain 'B' and resid 397 through 413 Processing helix chain 'B' and resid 475 through 482 Processing helix chain 'B' and resid 494 through 506 Processing helix chain 'B' and resid 521 through 529 Processing helix chain 'C' and resid 41 through 65 Processing helix chain 'C' and resid 69 through 84 Processing helix chain 'C' and resid 95 through 116 removed outlier: 3.617A pdb=" N PHE C 110 " --> pdb=" O HIS C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 140 Processing helix chain 'C' and resid 142 through 153 Processing helix chain 'C' and resid 218 through 242 removed outlier: 4.424A pdb=" N SER C 222 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 223 " --> pdb=" O ASP C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 removed outlier: 4.000A pdb=" N SER C 248 " --> pdb=" O PRO C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 278 through 289 removed outlier: 3.803A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY C 284 " --> pdb=" O GLU C 280 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 304 removed outlier: 3.696A pdb=" N LEU C 297 " --> pdb=" O CYS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 323 Processing helix chain 'C' and resid 325 through 339 Processing helix chain 'C' and resid 343 through 350 Processing helix chain 'C' and resid 351 through 359 removed outlier: 3.510A pdb=" N ILE C 355 " --> pdb=" O TYR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 379 Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'C' and resid 396 through 407 Processing helix chain 'C' and resid 410 through 423 Processing helix chain 'C' and resid 425 through 438 Processing helix chain 'C' and resid 449 through 461 Processing sheet with id=AA1, first strand: chain 'A' and resid 516 through 520 removed outlier: 9.435A pdb=" N VAL A 516 " --> pdb=" O TYR A 373 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER A 375 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ALA A 518 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N CYS A 377 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL A 520 " --> pdb=" O CYS A 377 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N SER A 379 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TYR A 360 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA A 348 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE A 362 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N TRP A 366 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ARG A 342 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 497 " --> pdb=" O TRP A 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 430 through 438 removed outlier: 7.663A pdb=" N GLU A 451 " --> pdb=" O PRO A 391 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N TYR A 388 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL A 476 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 390 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 394 through 397 removed outlier: 6.170A pdb=" N ARG A 395 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS A 402 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 609 through 612 removed outlier: 8.599A pdb=" N GLU A 610 " --> pdb=" O HIS A 582 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS A 584 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA A 612 " --> pdb=" O CYS A 584 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU A 586 " --> pdb=" O ALA A 612 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL A 558 " --> pdb=" O SER A 587 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LYS A 545 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE A 560 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER A 543 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA A 562 " --> pdb=" O SER A 541 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER A 541 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL A 564 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 539 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N HIS A 566 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL A 537 " --> pdb=" O HIS A 566 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A 634 " --> pdb=" O CYS A 691 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 849 through 851 removed outlier: 6.308A pdb=" N ILE A1036 " --> pdb=" O ASP A 859 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASP A 859 " --> pdb=" O ILE A1036 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY A1038 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER A1001 " --> pdb=" O GLY A 997 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY A 997 " --> pdb=" O SER A1001 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N MET A1003 " --> pdb=" O ILE A 995 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 851 removed outlier: 18.129A pdb=" N ASP A1037 " --> pdb=" O GLY A1060 " (cutoff:3.500A) removed outlier: 14.754A pdb=" N GLY A1060 " --> pdb=" O ASP A1037 " (cutoff:3.500A) removed outlier: 10.435A pdb=" N ILE A1039 " --> pdb=" O PRO A1058 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS A1041 " --> pdb=" O VAL A1056 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N VAL A1056 " --> pdb=" O LYS A1041 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU A1043 " --> pdb=" O LEU A1054 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU A1054 " --> pdb=" O LEU A1043 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU A1045 " --> pdb=" O ALA A1052 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ALA A1052 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LYS A1063 " --> pdb=" O THR A1059 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1131 through 1134 Processing sheet with id=AA8, first strand: chain 'A' and resid 1131 through 1134 Processing sheet with id=AA9, first strand: chain 'A' and resid 1276 through 1279 Processing sheet with id=AB1, first strand: chain 'A' and resid 1293 through 1294 Processing sheet with id=AB2, first strand: chain 'A' and resid 1353 through 1354 Processing sheet with id=AB3, first strand: chain 'A' and resid 1444 through 1446 Processing sheet with id=AB4, first strand: chain 'B' and resid 170 through 175 removed outlier: 6.573A pdb=" N VAL B 170 " --> pdb=" O ARG B 597 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG B 597 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B 592 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N THR B 570 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N CYS B 346 " --> pdb=" O THR B 570 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N MET B 341 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE B 376 " --> pdb=" O MET B 341 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE B 343 " --> pdb=" O ILE B 376 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU B 378 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA B 345 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS B 375 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL B 423 " --> pdb=" O CYS B 375 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU B 377 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 420 " --> pdb=" O HIS B 454 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 192 through 194 removed outlier: 6.591A pdb=" N VAL B 468 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE B 539 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY B 470 " --> pdb=" O ILE B 539 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 283 through 285 removed outlier: 6.429A pdb=" N GLU B 249 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY B 306 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL B 251 " --> pdb=" O MET B 304 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N MET B 304 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 253 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 302 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE B 303 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU B 319 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLU B 305 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AB8, first strand: chain 'B' and resid 563 through 564 720 hydrogen bonds defined for protein. 2028 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: 11.97 Time building geometry restraints manager: 8.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.13: 15078 1.13 - 1.42: 6317 1.42 - 1.70: 9019 1.70 - 1.99: 109 1.99 - 2.28: 12 Bond restraints: 30535 Sorted by residual: bond pdb=" CA ARG B 371 " pdb=" C ARG B 371 " ideal model delta sigma weight residual 1.531 1.523 0.009 7.40e-03 1.83e+04 1.36e+00 bond pdb=" CA ARG C 334 " pdb=" C ARG C 334 " ideal model delta sigma weight residual 1.524 1.511 0.014 1.28e-02 6.10e+03 1.17e+00 bond pdb=" CA PHE C 126 " pdb=" C PHE C 126 " ideal model delta sigma weight residual 1.524 1.510 0.014 1.32e-02 5.74e+03 1.07e+00 bond pdb=" CA LEU C 225 " pdb=" C LEU C 225 " ideal model delta sigma weight residual 1.523 1.511 0.012 1.30e-02 5.92e+03 8.79e-01 bond pdb=" CA ILE C 127 " pdb=" C ILE C 127 " ideal model delta sigma weight residual 1.524 1.513 0.011 1.22e-02 6.72e+03 8.22e-01 ... (remaining 30530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 50749 0.91 - 1.82: 4267 1.82 - 2.73: 182 2.73 - 3.64: 83 3.64 - 4.55: 24 Bond angle restraints: 55305 Sorted by residual: angle pdb=" N GLY A 363 " pdb=" CA GLY A 363 " pdb=" C GLY A 363 " ideal model delta sigma weight residual 111.08 114.78 -3.70 1.62e+00 3.81e-01 5.23e+00 angle pdb=" C LEU A 589 " pdb=" N ASN A 590 " pdb=" CA ASN A 590 " ideal model delta sigma weight residual 122.93 119.60 3.33 1.51e+00 4.39e-01 4.88e+00 angle pdb=" N LYS C 104 " pdb=" CA LYS C 104 " pdb=" C LYS C 104 " ideal model delta sigma weight residual 111.37 107.82 3.55 1.64e+00 3.72e-01 4.69e+00 angle pdb=" N ARG C 334 " pdb=" CA ARG C 334 " pdb=" C ARG C 334 " ideal model delta sigma weight residual 111.02 108.42 2.60 1.22e+00 6.72e-01 4.53e+00 angle pdb=" N THR C 338 " pdb=" CA THR C 338 " pdb=" C THR C 338 " ideal model delta sigma weight residual 112.38 110.00 2.38 1.22e+00 6.72e-01 3.82e+00 ... (remaining 55300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 12804 17.86 - 35.71: 1043 35.71 - 53.57: 387 53.57 - 71.42: 99 71.42 - 89.28: 27 Dihedral angle restraints: 14360 sinusoidal: 7884 harmonic: 6476 Sorted by residual: dihedral pdb=" CA ASP A 632 " pdb=" CB ASP A 632 " pdb=" CG ASP A 632 " pdb=" OD1 ASP A 632 " ideal model delta sinusoidal sigma weight residual -30.00 -86.10 56.10 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CB GLU B 273 " pdb=" CG GLU B 273 " pdb=" CD GLU B 273 " pdb=" OE1 GLU B 273 " ideal model delta sinusoidal sigma weight residual 0.00 -89.28 89.28 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 786 " pdb=" CG GLU A 786 " pdb=" CD GLU A 786 " pdb=" OE1 GLU A 786 " ideal model delta sinusoidal sigma weight residual 0.00 -88.82 88.82 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 14357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1381 0.027 - 0.053: 605 0.053 - 0.080: 162 0.080 - 0.106: 109 0.106 - 0.133: 52 Chirality restraints: 2309 Sorted by residual: chirality pdb=" CA ILE B 303 " pdb=" N ILE B 303 " pdb=" C ILE B 303 " pdb=" CB ILE B 303 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE A 501 " pdb=" N ILE A 501 " pdb=" C ILE A 501 " pdb=" CB ILE A 501 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE A1004 " pdb=" N ILE A1004 " pdb=" C ILE A1004 " pdb=" CB ILE A1004 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 2306 not shown) Planarity restraints: 4451 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 334 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C ARG C 334 " -0.051 2.00e-02 2.50e+03 pdb=" O ARG C 334 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU C 335 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 104 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.39e+00 pdb=" C LYS C 104 " -0.047 2.00e-02 2.50e+03 pdb=" O LYS C 104 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP C 105 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 332 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C PHE C 332 " -0.038 2.00e-02 2.50e+03 pdb=" O PHE C 332 " 0.014 2.00e-02 2.50e+03 pdb=" N TRP C 333 " 0.013 2.00e-02 2.50e+03 ... (remaining 4448 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 575 2.12 - 2.74: 54545 2.74 - 3.36: 86822 3.36 - 3.98: 112181 3.98 - 4.60: 175850 Nonbonded interactions: 429973 Sorted by model distance: nonbonded pdb=" O LEU B 525 " pdb=" HG1 THR B 529 " model vdw 1.497 2.450 nonbonded pdb=" O LEU A1135 " pdb=" H GLY A1168 " model vdw 1.554 2.450 nonbonded pdb="HH11 ARG A 667 " pdb=" O ASN A 683 " model vdw 1.591 2.450 nonbonded pdb=" O GLN A 397 " pdb=" H GLY A 401 " model vdw 1.596 2.450 nonbonded pdb="HH21 ARG C 51 " pdb=" OD1 ASP C 105 " model vdw 1.639 2.450 ... (remaining 429968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 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: 0.470 Extract box with map and model: 0.990 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 83.380 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 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 : 0.003 0.084 15438 Z= 0.153 Angle : 0.479 7.998 20887 Z= 0.258 Chirality : 0.039 0.133 2309 Planarity : 0.003 0.031 2682 Dihedral : 16.851 89.277 5844 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 16.16 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 1855 helix: 0.75 (0.19), residues: 796 sheet: 0.78 (0.31), residues: 259 loop : 0.03 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 746 HIS 0.004 0.001 HIS A 974 PHE 0.013 0.001 PHE C 332 TYR 0.013 0.001 TYR C 453 ARG 0.002 0.000 ARG A 977 Details of bonding type rmsd hydrogen bonds : bond 0.12697 ( 712) hydrogen bonds : angle 6.62227 ( 2028) metal coordination : bond 0.04902 ( 12) metal coordination : angle 3.26302 ( 24) covalent geometry : bond 0.00315 (15426) covalent geometry : angle 0.46667 (20863) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 2.567 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 5.4820 time to fit residues: 1030.7722 Evaluate side-chains 67 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 5.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 707 HIS A 861 ASN A 869 GLN A 937 GLN A1026 ASN A1107 ASN A1435 GLN C 331 GLN C 405 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.049669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.037730 restraints weight = 133255.287| |-----------------------------------------------------------------------------| r_work (start): 0.2547 rms_B_bonded: 2.94 r_work: 0.2415 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2296 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15438 Z= 0.177 Angle : 0.545 8.163 20887 Z= 0.280 Chirality : 0.040 0.132 2309 Planarity : 0.004 0.042 2682 Dihedral : 4.043 20.643 2041 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.06 % Allowed : 18.63 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.20), residues: 1855 helix: 1.60 (0.19), residues: 795 sheet: 0.84 (0.31), residues: 259 loop : -0.06 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 746 HIS 0.003 0.001 HIS B 501 PHE 0.011 0.001 PHE C 332 TYR 0.012 0.001 TYR A 732 ARG 0.006 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 712) hydrogen bonds : angle 4.94860 ( 2028) metal coordination : bond 0.00736 ( 12) metal coordination : angle 2.98141 ( 24) covalent geometry : bond 0.00396 (15426) covalent geometry : angle 0.53590 (20863) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 2.187 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: symmetry clash REVERT: A 727 ASN cc_start: 0.9634 (OUTLIER) cc_final: 0.9361 (m-40) REVERT: B 392 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9192 (mm) REVERT: C 217 HIS cc_start: 0.5318 (m90) cc_final: 0.4933 (m90) REVERT: C 405 GLN cc_start: 0.9438 (OUTLIER) cc_final: 0.9186 (mt0) outliers start: 18 outliers final: 2 residues processed: 82 average time/residue: 3.1556 time to fit residues: 285.3200 Evaluate side-chains 62 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 405 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 96 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 18 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 = 0.2877 r_free = 0.2877 target = 0.048784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.036818 restraints weight = 135659.992| |-----------------------------------------------------------------------------| r_work (start): 0.2517 rms_B_bonded: 2.96 r_work: 0.2386 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2268 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15438 Z= 0.198 Angle : 0.526 9.199 20887 Z= 0.266 Chirality : 0.040 0.131 2309 Planarity : 0.003 0.030 2682 Dihedral : 4.030 19.304 2041 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.65 % Allowed : 18.63 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.20), residues: 1855 helix: 1.83 (0.19), residues: 795 sheet: 0.77 (0.31), residues: 262 loop : -0.08 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 746 HIS 0.004 0.001 HIS A1324 PHE 0.011 0.001 PHE C 149 TYR 0.011 0.001 TYR A 732 ARG 0.006 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 712) hydrogen bonds : angle 4.71172 ( 2028) metal coordination : bond 0.01039 ( 12) metal coordination : angle 3.18956 ( 24) covalent geometry : bond 0.00446 (15426) covalent geometry : angle 0.51456 (20863) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 2.645 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: A 411 MET cc_start: 0.9274 (tpt) cc_final: 0.8901 (tpp) REVERT: A 727 ASN cc_start: 0.9612 (OUTLIER) cc_final: 0.9356 (m-40) outliers start: 11 outliers final: 2 residues processed: 73 average time/residue: 3.2927 time to fit residues: 266.1717 Evaluate side-chains 59 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain C residue 232 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 25 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.048558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.036405 restraints weight = 135788.635| |-----------------------------------------------------------------------------| r_work (start): 0.2513 rms_B_bonded: 2.96 r_work: 0.2381 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2263 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15438 Z= 0.167 Angle : 0.514 9.683 20887 Z= 0.257 Chirality : 0.040 0.130 2309 Planarity : 0.003 0.031 2682 Dihedral : 3.966 19.216 2041 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.77 % Allowed : 18.34 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.20), residues: 1855 helix: 1.94 (0.19), residues: 795 sheet: 0.77 (0.31), residues: 260 loop : -0.05 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 746 HIS 0.003 0.001 HIS A1324 PHE 0.010 0.001 PHE C 44 TYR 0.011 0.001 TYR A 732 ARG 0.004 0.000 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 712) hydrogen bonds : angle 4.55842 ( 2028) metal coordination : bond 0.00827 ( 12) metal coordination : angle 3.34105 ( 24) covalent geometry : bond 0.00376 (15426) covalent geometry : angle 0.50157 (20863) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 2.234 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: A 411 MET cc_start: 0.9262 (tpt) cc_final: 0.8885 (tpp) REVERT: A 511 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8764 (ptt) REVERT: A 727 ASN cc_start: 0.9612 (OUTLIER) cc_final: 0.9349 (m-40) REVERT: A 798 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8527 (mp0) outliers start: 13 outliers final: 6 residues processed: 68 average time/residue: 3.1011 time to fit residues: 233.9913 Evaluate side-chains 63 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1181 ASN Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 405 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 97 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.047971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.035874 restraints weight = 136449.564| |-----------------------------------------------------------------------------| r_work (start): 0.2495 rms_B_bonded: 2.94 r_work: 0.2365 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2247 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15438 Z= 0.203 Angle : 0.518 10.508 20887 Z= 0.259 Chirality : 0.040 0.129 2309 Planarity : 0.003 0.033 2682 Dihedral : 3.987 17.921 2041 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.00 % Allowed : 17.87 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.20), residues: 1855 helix: 2.00 (0.19), residues: 794 sheet: 0.64 (0.31), residues: 266 loop : -0.07 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 746 HIS 0.004 0.001 HIS A1152 PHE 0.013 0.001 PHE C 228 TYR 0.010 0.001 TYR A 732 ARG 0.005 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 712) hydrogen bonds : angle 4.51254 ( 2028) metal coordination : bond 0.01039 ( 12) metal coordination : angle 3.57127 ( 24) covalent geometry : bond 0.00458 (15426) covalent geometry : angle 0.50374 (20863) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 MET cc_start: 0.9278 (tpt) cc_final: 0.8898 (tpp) REVERT: A 798 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8446 (mp0) outliers start: 17 outliers final: 6 residues processed: 70 average time/residue: 3.0665 time to fit residues: 239.5994 Evaluate side-chains 59 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1181 ASN Chi-restraints excluded: chain A residue 1378 SER Chi-restraints excluded: chain C residue 396 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 126 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 131 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN A1193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.048815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.036798 restraints weight = 135778.800| |-----------------------------------------------------------------------------| r_work (start): 0.2525 rms_B_bonded: 2.93 r_work: 0.2395 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2278 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15438 Z= 0.106 Angle : 0.486 10.348 20887 Z= 0.241 Chirality : 0.039 0.133 2309 Planarity : 0.003 0.036 2682 Dihedral : 3.859 17.262 2041 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.83 % Allowed : 17.98 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.20), residues: 1855 helix: 2.15 (0.19), residues: 795 sheet: 0.70 (0.31), residues: 260 loop : 0.01 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 746 HIS 0.003 0.001 HIS C 394 PHE 0.014 0.001 PHE C 228 TYR 0.009 0.001 TYR A 732 ARG 0.004 0.000 ARG A1163 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 712) hydrogen bonds : angle 4.33375 ( 2028) metal coordination : bond 0.00538 ( 12) metal coordination : angle 3.48197 ( 24) covalent geometry : bond 0.00243 (15426) covalent geometry : angle 0.47131 (20863) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 2.373 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: A 411 MET cc_start: 0.9271 (tpt) cc_final: 0.8881 (tpp) REVERT: A 798 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8491 (mp0) REVERT: C 405 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8689 (mt0) outliers start: 14 outliers final: 4 residues processed: 66 average time/residue: 3.0053 time to fit residues: 220.6824 Evaluate side-chains 54 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1181 ASN Chi-restraints excluded: chain C residue 405 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 175 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.047786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.035747 restraints weight = 137350.924| |-----------------------------------------------------------------------------| r_work (start): 0.2497 rms_B_bonded: 2.94 r_work: 0.2367 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2252 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15438 Z= 0.207 Angle : 0.510 11.359 20887 Z= 0.253 Chirality : 0.040 0.130 2309 Planarity : 0.003 0.033 2682 Dihedral : 3.900 17.548 2041 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.59 % Allowed : 17.87 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.20), residues: 1855 helix: 2.15 (0.19), residues: 794 sheet: 0.64 (0.31), residues: 264 loop : -0.02 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 746 HIS 0.003 0.001 HIS A1324 PHE 0.009 0.001 PHE C 44 TYR 0.010 0.001 TYR B 522 ARG 0.004 0.000 ARG A1163 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 712) hydrogen bonds : angle 4.41581 ( 2028) metal coordination : bond 0.01035 ( 12) metal coordination : angle 3.74106 ( 24) covalent geometry : bond 0.00465 (15426) covalent geometry : angle 0.49415 (20863) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 MET cc_start: 0.9275 (tpt) cc_final: 0.8894 (tpp) REVERT: A 798 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8454 (mp0) REVERT: C 405 GLN cc_start: 0.9231 (OUTLIER) cc_final: 0.8749 (mt0) outliers start: 10 outliers final: 5 residues processed: 58 average time/residue: 3.4166 time to fit residues: 219.4150 Evaluate side-chains 56 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1181 ASN Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 405 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.2856 r_free = 0.2856 target = 0.047979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.035990 restraints weight = 135502.924| |-----------------------------------------------------------------------------| r_work (start): 0.2505 rms_B_bonded: 2.91 r_work: 0.2378 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2264 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15438 Z= 0.166 Angle : 0.502 11.937 20887 Z= 0.249 Chirality : 0.040 0.131 2309 Planarity : 0.003 0.040 2682 Dihedral : 3.876 17.237 2041 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.47 % Allowed : 18.04 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.20), residues: 1855 helix: 2.21 (0.19), residues: 794 sheet: 0.64 (0.31), residues: 260 loop : 0.02 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 746 HIS 0.003 0.001 HIS A1152 PHE 0.010 0.001 PHE C 44 TYR 0.009 0.001 TYR A 732 ARG 0.004 0.000 ARG A1163 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 712) hydrogen bonds : angle 4.36401 ( 2028) metal coordination : bond 0.00854 ( 12) metal coordination : angle 3.85145 ( 24) covalent geometry : bond 0.00378 (15426) covalent geometry : angle 0.48474 (20863) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 MET cc_start: 0.9265 (tpt) cc_final: 0.8879 (tpp) REVERT: A 798 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8455 (mp0) outliers start: 8 outliers final: 6 residues processed: 58 average time/residue: 3.4990 time to fit residues: 225.5661 Evaluate side-chains 55 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1181 ASN Chi-restraints excluded: chain A residue 1378 SER Chi-restraints excluded: chain C residue 396 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 14 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.047559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.035607 restraints weight = 135780.675| |-----------------------------------------------------------------------------| r_work (start): 0.2494 rms_B_bonded: 2.90 r_work: 0.2367 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2253 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15438 Z= 0.214 Angle : 0.513 12.387 20887 Z= 0.255 Chirality : 0.040 0.130 2309 Planarity : 0.003 0.057 2682 Dihedral : 3.907 17.703 2041 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.53 % Allowed : 17.87 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.20), residues: 1855 helix: 2.19 (0.19), residues: 794 sheet: 0.57 (0.31), residues: 264 loop : 0.01 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 746 HIS 0.003 0.001 HIS A1324 PHE 0.010 0.001 PHE C 44 TYR 0.010 0.001 TYR A 732 ARG 0.008 0.000 ARG A1163 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 712) hydrogen bonds : angle 4.41096 ( 2028) metal coordination : bond 0.01078 ( 12) metal coordination : angle 3.96688 ( 24) covalent geometry : bond 0.00483 (15426) covalent geometry : angle 0.49555 (20863) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 MET cc_start: 0.9252 (tpt) cc_final: 0.8844 (tpp) REVERT: A 798 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8462 (mp0) outliers start: 9 outliers final: 4 residues processed: 56 average time/residue: 3.1182 time to fit residues: 194.6140 Evaluate side-chains 53 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1378 SER Chi-restraints excluded: chain C residue 396 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.2859 r_free = 0.2859 target = 0.047840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.035906 restraints weight = 135411.344| |-----------------------------------------------------------------------------| r_work (start): 0.2493 rms_B_bonded: 2.92 r_work: 0.2365 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2251 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9075 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15438 Z= 0.205 Angle : 0.518 12.939 20887 Z= 0.257 Chirality : 0.040 0.131 2309 Planarity : 0.003 0.033 2682 Dihedral : 3.922 17.854 2041 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.29 % Allowed : 18.04 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.20), residues: 1855 helix: 2.18 (0.19), residues: 794 sheet: 0.56 (0.31), residues: 264 loop : 0.02 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 746 HIS 0.004 0.001 HIS A 982 PHE 0.010 0.001 PHE C 44 TYR 0.011 0.001 TYR A 596 ARG 0.004 0.000 ARG A1163 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 712) hydrogen bonds : angle 4.40682 ( 2028) metal coordination : bond 0.01060 ( 12) metal coordination : angle 4.14080 ( 24) covalent geometry : bond 0.00464 (15426) covalent geometry : angle 0.49883 (20863) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 MET cc_start: 0.9255 (tpt) cc_final: 0.8852 (tpp) REVERT: A 798 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8445 (mp0) outliers start: 5 outliers final: 4 residues processed: 53 average time/residue: 3.3071 time to fit residues: 195.0722 Evaluate side-chains 52 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1378 SER Chi-restraints excluded: chain C residue 396 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 0.0170 chunk 53 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 170 optimal weight: 0.0670 chunk 2 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.048099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.036153 restraints weight = 134908.446| |-----------------------------------------------------------------------------| r_work (start): 0.2512 rms_B_bonded: 2.90 r_work: 0.2385 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2271 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15438 Z= 0.122 Angle : 0.495 12.718 20887 Z= 0.244 Chirality : 0.039 0.133 2309 Planarity : 0.003 0.056 2682 Dihedral : 3.851 16.467 2041 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.29 % Allowed : 18.10 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.20), residues: 1855 helix: 2.30 (0.19), residues: 788 sheet: 0.61 (0.31), residues: 260 loop : 0.10 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 746 HIS 0.003 0.001 HIS A1152 PHE 0.010 0.001 PHE C 44 TYR 0.012 0.001 TYR A 596 ARG 0.007 0.000 ARG A1163 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 712) hydrogen bonds : angle 4.28872 ( 2028) metal coordination : bond 0.00672 ( 12) metal coordination : angle 4.00723 ( 24) covalent geometry : bond 0.00280 (15426) covalent geometry : angle 0.47643 (20863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17692.55 seconds wall clock time: 305 minutes 11.54 seconds (18311.54 seconds total)