Starting phenix.real_space_refine on Fri Jan 19 17:43:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdg_29011/01_2024/8fdg_29011.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdg_29011/01_2024/8fdg_29011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdg_29011/01_2024/8fdg_29011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdg_29011/01_2024/8fdg_29011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdg_29011/01_2024/8fdg_29011.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdg_29011/01_2024/8fdg_29011.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 55 5.16 5 C 7707 2.51 5 N 2064 2.21 5 O 2337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1461": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12163 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 12163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1505, 12163 Classifications: {'peptide': 1505} Link IDs: {'PTRANS': 76, 'TRANS': 1428} Time building chain proxies: 6.48, per 1000 atoms: 0.53 Number of scatterers: 12163 At special positions: 0 Unit cell: (92.7, 110.7, 142.2, 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 55 16.00 O 2337 8.00 N 2064 7.00 C 7707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 472 " - pdb=" SG CYS A 498 " distance=2.05 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 656 " distance=2.03 Simple disulfide: pdb=" SG CYS A 994 " - pdb=" SG CYS A1020 " distance=2.04 Simple disulfide: pdb=" SG CYS A1176 " - pdb=" SG CYS A1330 " distance=2.03 Simple disulfide: pdb=" SG CYS A1335 " - pdb=" SG CYS A1490 " distance=2.04 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: 4.36 Conformation dependent library (CDL) restraints added in 2.4 seconds 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2838 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 21 sheets defined 5.1% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 149 through 155 removed outlier: 3.686A pdb=" N PHE A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.786A pdb=" N ALA A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 464 removed outlier: 3.667A pdb=" N GLU A 464 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 removed outlier: 3.516A pdb=" N SER A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 539 removed outlier: 3.545A pdb=" N ASN A 534 " --> pdb=" O TYR A 530 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N CYS A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 760 through 764 removed outlier: 4.281A pdb=" N SER A 764 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 986 Processing helix chain 'A' and resid 1057 through 1062 Processing helix chain 'A' and resid 1188 through 1190 No H-bonds generated for 'chain 'A' and resid 1188 through 1190' Processing helix chain 'A' and resid 1203 through 1207 removed outlier: 3.877A pdb=" N ALA A1206 " --> pdb=" O PRO A1203 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG A1207 " --> pdb=" O ARG A1204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1203 through 1207' Processing helix chain 'A' and resid 1501 through 1505 removed outlier: 3.889A pdb=" N LYS A1505 " --> pdb=" O ILE A1502 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 6.163A pdb=" N ARG A 4 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 40 removed outlier: 3.759A pdb=" N LYS A 75 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 10 " --> pdb=" O LYS A 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 65 Processing sheet with id=AA4, first strand: chain 'A' and resid 181 through 185 removed outlier: 3.725A pdb=" N LYS A 181 " --> pdb=" O HIS A 224 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN A 269 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A 249 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 191 Processing sheet with id=AA6, first strand: chain 'A' and resid 217 through 219 removed outlier: 6.178A pdb=" N ILE A 217 " --> pdb=" O ASP A 297 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY A 276 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 363 through 370 removed outlier: 3.650A pdb=" N LYS A 408 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 328 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 410 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU A 330 " --> pdb=" O MET A 410 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP A 401 " --> pdb=" O ILE A 459 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 395 through 397 removed outlier: 6.696A pdb=" N ILE A 395 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N CYS A 498 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA A 397 " --> pdb=" O CYS A 498 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 478 " --> pdb=" O TYR A 418 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 511 through 515 removed outlier: 7.221A pdb=" N THR A 579 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASP A 513 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 581 " --> pdb=" O ASP A 513 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 515 " --> pdb=" O GLN A 581 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N HIS A 583 " --> pdb=" O GLU A 515 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 520 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 511 through 515 removed outlier: 7.221A pdb=" N THR A 579 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASP A 513 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 581 " --> pdb=" O ASP A 513 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 515 " --> pdb=" O GLN A 581 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N HIS A 583 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 572 through 575 removed outlier: 6.675A pdb=" N LEU A 572 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL A 654 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE A 574 " --> pdb=" O VAL A 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 594 through 596 removed outlier: 3.680A pdb=" N LEU A 594 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 883 through 891 removed outlier: 6.194A pdb=" N ARG A 849 " --> pdb=" O GLN A 926 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ARG A 928 " --> pdb=" O ARG A 849 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR A 851 " --> pdb=" O ARG A 928 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N LYS A 930 " --> pdb=" O TYR A 851 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE A 853 " --> pdb=" O LYS A 930 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A 973 " --> pdb=" O ASN A 931 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 917 through 920 removed outlier: 6.322A pdb=" N ILE A 917 " --> pdb=" O LEU A1018 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N CYS A1020 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA A 919 " --> pdb=" O CYS A1020 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A1019 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG A 995 " --> pdb=" O ILE A1019 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1036 through 1041 removed outlier: 4.456A pdb=" N ARG A1036 " --> pdb=" O TRP A1094 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1088 through 1089 removed outlier: 3.750A pdb=" N MET A1089 " --> pdb=" O LEU A1170 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN A1154 " --> pdb=" O HIS A1112 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP A1131 " --> pdb=" O VAL A1111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1119 through 1120 Processing sheet with id=AB9, first strand: chain 'A' and resid 1178 through 1179 removed outlier: 3.677A pdb=" N MET A1178 " --> pdb=" O GLY A1329 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU A1326 " --> pdb=" O ILE A1245 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE A1245 " --> pdb=" O GLU A1326 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLN A1328 " --> pdb=" O THR A1243 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLN A1233 " --> pdb=" O ARG A1311 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG A1311 " --> pdb=" O GLN A1233 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASP A1235 " --> pdb=" O TYR A1309 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYR A1309 " --> pdb=" O ASP A1235 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN A1237 " --> pdb=" O ALA A1307 " (cutoff:3.500A) removed outlier: 10.807A pdb=" N ALA A1307 " --> pdb=" O GLN A1237 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N GLU A1239 " --> pdb=" O ILE A1305 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N ILE A1305 " --> pdb=" O GLU A1239 " (cutoff:3.500A) removed outlier: 10.112A pdb=" N ILE A1241 " --> pdb=" O PRO A1303 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N THR A1243 " --> pdb=" O PHE A1301 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A1245 " --> pdb=" O ASN A1299 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE A1310 " --> pdb=" O TYR A1266 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR A1266 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE A1312 " --> pdb=" O VAL A1264 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A1264 " --> pdb=" O ILE A1312 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N PHE A1262 " --> pdb=" O PRO A1314 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG A1316 " --> pdb=" O THR A1260 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1192 through 1193 removed outlier: 7.022A pdb=" N GLN A1233 " --> pdb=" O ARG A1311 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG A1311 " --> pdb=" O GLN A1233 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASP A1235 " --> pdb=" O TYR A1309 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYR A1309 " --> pdb=" O ASP A1235 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN A1237 " --> pdb=" O ALA A1307 " (cutoff:3.500A) removed outlier: 10.807A pdb=" N ALA A1307 " --> pdb=" O GLN A1237 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N GLU A1239 " --> pdb=" O ILE A1305 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N ILE A1305 " --> pdb=" O GLU A1239 " (cutoff:3.500A) removed outlier: 10.112A pdb=" N ILE A1241 " --> pdb=" O PRO A1303 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N THR A1243 " --> pdb=" O PHE A1301 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A1245 " --> pdb=" O ASN A1299 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE A1310 " --> pdb=" O TYR A1266 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR A1266 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE A1312 " --> pdb=" O VAL A1264 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A1264 " --> pdb=" O ILE A1312 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N PHE A1262 " --> pdb=" O PRO A1314 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG A1316 " --> pdb=" O THR A1260 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A1266 " --> pdb=" O GLN A1274 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1217 through 1218 removed outlier: 3.820A pdb=" N TRP A1217 " --> pdb=" O LEU A1323 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A1323 " --> pdb=" O TRP A1217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 1434 through 1435 removed outlier: 3.730A pdb=" N TYR A1426 " --> pdb=" O LYS A1434 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL A1419 " --> pdb=" O TRP A1477 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TRP A1477 " --> pdb=" O VAL A1419 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER A1421 " --> pdb=" O LYS A1475 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A1427 " --> pdb=" O PHE A1469 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE A1469 " --> pdb=" O SER A1427 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A1461 " --> pdb=" O THR A1403 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THR A1403 " --> pdb=" O PHE A1461 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N LYS A1401 " --> pdb=" O PRO A1463 " (cutoff:3.500A) removed outlier: 10.790A pdb=" N ILE A1465 " --> pdb=" O ILE A1399 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N ILE A1399 " --> pdb=" O ILE A1465 " (cutoff:3.500A) removed outlier: 9.690A pdb=" N SER A1467 " --> pdb=" O LEU A1397 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU A1397 " --> pdb=" O SER A1467 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE A1469 " --> pdb=" O ASP A1395 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASP A1395 " --> pdb=" O PHE A1469 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ARG A1471 " --> pdb=" O GLU A1393 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU A1393 " --> pdb=" O ARG A1471 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE A1488 " --> pdb=" O THR A1403 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ILE A1405 " --> pdb=" O GLU A1486 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLU A1486 " --> pdb=" O ILE A1405 " (cutoff:3.500A) 193 hydrogen bonds defined for protein. 483 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.88 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3967 1.34 - 1.47: 3113 1.47 - 1.60: 5305 1.60 - 1.72: 0 1.72 - 1.85: 92 Bond restraints: 12477 Sorted by residual: bond pdb=" C ILE A 339 " pdb=" N PRO A 340 " ideal model delta sigma weight residual 1.330 1.364 -0.034 1.22e-02 6.72e+03 7.96e+00 bond pdb=" CA GLU A 907 " pdb=" CB GLU A 907 " ideal model delta sigma weight residual 1.526 1.562 -0.035 1.76e-02 3.23e+03 4.05e+00 bond pdb=" N GLU A1494 " pdb=" CA GLU A1494 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.10e-02 8.26e+03 3.17e+00 bond pdb=" CB CYS A 498 " pdb=" SG CYS A 498 " ideal model delta sigma weight residual 1.808 1.848 -0.040 3.30e-02 9.18e+02 1.47e+00 bond pdb=" C PRO A 670 " pdb=" N PRO A 671 " ideal model delta sigma weight residual 1.334 1.360 -0.027 2.34e-02 1.83e+03 1.29e+00 ... (remaining 12472 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.83: 412 106.83 - 113.64: 6666 113.64 - 120.44: 4498 120.44 - 127.24: 5171 127.24 - 134.04: 167 Bond angle restraints: 16914 Sorted by residual: angle pdb=" C ARG A1282 " pdb=" N ASN A1283 " pdb=" CA ASN A1283 " ideal model delta sigma weight residual 121.54 132.50 -10.96 1.91e+00 2.74e-01 3.29e+01 angle pdb=" N VAL A1033 " pdb=" CA VAL A1033 " pdb=" C VAL A1033 " ideal model delta sigma weight residual 113.53 110.14 3.39 9.80e-01 1.04e+00 1.20e+01 angle pdb=" CA ILE A 878 " pdb=" C ILE A 878 " pdb=" N PRO A 879 " ideal model delta sigma weight residual 116.57 119.65 -3.08 9.80e-01 1.04e+00 9.85e+00 angle pdb=" C VAL A1332 " pdb=" N ASN A1333 " pdb=" CA ASN A1333 " ideal model delta sigma weight residual 121.54 127.50 -5.96 1.91e+00 2.74e-01 9.75e+00 angle pdb=" CA CYS A 472 " pdb=" CB CYS A 472 " pdb=" SG CYS A 472 " ideal model delta sigma weight residual 114.40 121.35 -6.95 2.30e+00 1.89e-01 9.12e+00 ... (remaining 16909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 6776 17.70 - 35.41: 600 35.41 - 53.11: 82 53.11 - 70.81: 26 70.81 - 88.52: 17 Dihedral angle restraints: 7501 sinusoidal: 3085 harmonic: 4416 Sorted by residual: dihedral pdb=" CB CYS A 575 " pdb=" SG CYS A 575 " pdb=" SG CYS A 656 " pdb=" CB CYS A 656 " ideal model delta sinusoidal sigma weight residual 93.00 145.34 -52.34 1 1.00e+01 1.00e-02 3.73e+01 dihedral pdb=" CB CYS A 994 " pdb=" SG CYS A 994 " pdb=" SG CYS A1020 " pdb=" CB CYS A1020 " ideal model delta sinusoidal sigma weight residual 93.00 46.99 46.01 1 1.00e+01 1.00e-02 2.93e+01 dihedral pdb=" CB CYS A 472 " pdb=" SG CYS A 472 " pdb=" SG CYS A 498 " pdb=" CB CYS A 498 " ideal model delta sinusoidal sigma weight residual 93.00 47.59 45.41 1 1.00e+01 1.00e-02 2.86e+01 ... (remaining 7498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1174 0.038 - 0.075: 403 0.075 - 0.112: 156 0.112 - 0.150: 50 0.150 - 0.187: 6 Chirality restraints: 1789 Sorted by residual: chirality pdb=" CB ILE A 604 " pdb=" CA ILE A 604 " pdb=" CG1 ILE A 604 " pdb=" CG2 ILE A 604 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CB ILE A1019 " pdb=" CA ILE A1019 " pdb=" CG1 ILE A1019 " pdb=" CG2 ILE A1019 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.00e-01 chirality pdb=" CA PHE A1368 " pdb=" N PHE A1368 " pdb=" C PHE A1368 " pdb=" CB PHE A1368 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 1786 not shown) Planarity restraints: 2194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A1493 " 0.017 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C TYR A1493 " -0.056 2.00e-02 2.50e+03 pdb=" O TYR A1493 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU A1494 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 20 " 0.037 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO A 21 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1337 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO A1338 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A1338 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1338 " -0.030 5.00e-02 4.00e+02 ... (remaining 2191 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 501 2.71 - 3.26: 11655 3.26 - 3.81: 17400 3.81 - 4.35: 21212 4.35 - 4.90: 37298 Nonbonded interactions: 88066 Sorted by model distance: nonbonded pdb=" OG SER A1267 " pdb=" O ASN A1269 " model vdw 2.166 2.440 nonbonded pdb=" OE1 GLU A 372 " pdb=" OG1 THR A 380 " model vdw 2.181 2.440 nonbonded pdb=" OG SER A 92 " pdb=" OE2 GLU A1494 " model vdw 2.185 2.440 nonbonded pdb=" OD1 ASN A1215 " pdb=" NE2 HIS A1252 " model vdw 2.229 2.520 nonbonded pdb=" O ASN A 432 " pdb=" OG1 THR A 436 " model vdw 2.233 2.440 ... (remaining 88061 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 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: 1.920 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: 0.010 Extract box with map and model: 8.390 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 34.660 Find NCS groups from input model: 0.320 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 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 0.047 12477 Z= 0.178 Angle : 0.682 10.961 16914 Z= 0.371 Chirality : 0.047 0.187 1789 Planarity : 0.005 0.055 2194 Dihedral : 13.998 88.518 4642 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.91 % Favored : 88.09 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.20), residues: 1503 helix: -2.47 (0.65), residues: 42 sheet: -0.11 (0.25), residues: 440 loop : -2.88 (0.17), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1391 HIS 0.004 0.001 HIS A 318 PHE 0.017 0.001 PHE A1368 TYR 0.017 0.001 TYR A 840 ARG 0.006 0.000 ARG A 935 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.528 Fit side-chains revert: symmetry clash REVERT: A 375 SER cc_start: 0.8051 (m) cc_final: 0.7701 (p) REVERT: A 382 ASN cc_start: 0.7130 (m-40) cc_final: 0.6680 (m110) REVERT: A 400 ARG cc_start: 0.8266 (mtm110) cc_final: 0.7739 (ptm-80) REVERT: A 610 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7136 (mm-30) REVERT: A 759 MET cc_start: 0.2996 (mmm) cc_final: 0.0835 (ttt) REVERT: A 847 ASN cc_start: 0.7647 (m-40) cc_final: 0.7419 (m-40) REVERT: A 1031 MET cc_start: 0.7629 (mmt) cc_final: 0.7410 (mmt) REVERT: A 1366 GLU cc_start: 0.7895 (tt0) cc_final: 0.7558 (tt0) REVERT: A 1381 TRP cc_start: 0.6620 (p90) cc_final: 0.6326 (p90) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2496 time to fit residues: 61.6539 Evaluate side-chains 106 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 76 optimal weight: 0.0870 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 HIS ** A1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1496 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 12477 Z= 0.282 Angle : 0.720 8.550 16914 Z= 0.379 Chirality : 0.049 0.289 1789 Planarity : 0.005 0.065 2194 Dihedral : 6.107 26.930 1648 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.77 % Favored : 86.23 % Rotamer: Outliers : 1.71 % Allowed : 6.98 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.20), residues: 1503 helix: -2.12 (0.71), residues: 48 sheet: -0.11 (0.25), residues: 416 loop : -2.93 (0.17), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1391 HIS 0.006 0.001 HIS A 609 PHE 0.018 0.002 PHE A 771 TYR 0.024 0.002 TYR A 840 ARG 0.004 0.000 ARG A 935 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 1.421 Fit side-chains revert: symmetry clash REVERT: A 375 SER cc_start: 0.7722 (m) cc_final: 0.7510 (p) REVERT: A 400 ARG cc_start: 0.8344 (mtm110) cc_final: 0.7772 (ptm-80) REVERT: A 610 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7168 (mm-30) REVERT: A 645 LYS cc_start: 0.7677 (mttp) cc_final: 0.7212 (mttp) REVERT: A 847 ASN cc_start: 0.7841 (m-40) cc_final: 0.7558 (m-40) REVERT: A 857 GLU cc_start: 0.7221 (tt0) cc_final: 0.6906 (tt0) REVERT: A 1031 MET cc_start: 0.7687 (mmt) cc_final: 0.7476 (mmt) REVERT: A 1143 MET cc_start: 0.8529 (ttp) cc_final: 0.8290 (ttp) REVERT: A 1365 TRP cc_start: 0.7241 (m100) cc_final: 0.6973 (m100) REVERT: A 1366 GLU cc_start: 0.8124 (tt0) cc_final: 0.7449 (tp30) REVERT: A 1381 TRP cc_start: 0.6821 (p90) cc_final: 0.6614 (p90) outliers start: 23 outliers final: 19 residues processed: 127 average time/residue: 0.2329 time to fit residues: 44.5811 Evaluate side-chains 118 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 967 ASN Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1172 MET Chi-restraints excluded: chain A residue 1215 ASN Chi-restraints excluded: chain A residue 1412 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 0.0470 chunk 113 optimal weight: 0.0670 chunk 92 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 136 optimal weight: 0.5980 chunk 147 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 211 ASN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 12477 Z= 0.186 Angle : 0.641 10.397 16914 Z= 0.338 Chirality : 0.047 0.266 1789 Planarity : 0.005 0.054 2194 Dihedral : 5.829 26.705 1648 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.04 % Favored : 87.96 % Rotamer: Outliers : 2.00 % Allowed : 10.10 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.20), residues: 1503 helix: -1.87 (0.74), residues: 42 sheet: -0.14 (0.25), residues: 418 loop : -2.89 (0.17), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1361 HIS 0.005 0.001 HIS A 318 PHE 0.013 0.001 PHE A 771 TYR 0.021 0.001 TYR A1200 ARG 0.003 0.000 ARG A 935 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 1.485 Fit side-chains revert: symmetry clash REVERT: A 375 SER cc_start: 0.7696 (m) cc_final: 0.7432 (p) REVERT: A 400 ARG cc_start: 0.8299 (mtm110) cc_final: 0.7747 (ptm-80) REVERT: A 610 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7094 (mm-30) REVERT: A 645 LYS cc_start: 0.7635 (mttp) cc_final: 0.7165 (mttp) REVERT: A 759 MET cc_start: 0.2895 (mmm) cc_final: 0.0270 (ttt) REVERT: A 847 ASN cc_start: 0.7771 (m-40) cc_final: 0.7491 (m-40) REVERT: A 1341 MET cc_start: 0.5488 (tpt) cc_final: 0.5215 (tpt) REVERT: A 1365 TRP cc_start: 0.7002 (m100) cc_final: 0.6766 (m100) REVERT: A 1366 GLU cc_start: 0.8076 (tt0) cc_final: 0.7419 (tp30) outliers start: 27 outliers final: 17 residues processed: 122 average time/residue: 0.2192 time to fit residues: 41.4688 Evaluate side-chains 110 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 845 ASN Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 967 ASN Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1172 MET Chi-restraints excluded: chain A residue 1215 ASN Chi-restraints excluded: chain A residue 1450 ASN Chi-restraints excluded: chain A residue 1452 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 70 optimal weight: 30.0000 chunk 15 optimal weight: 0.0570 chunk 65 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 0.0000 chunk 144 optimal weight: 4.9990 chunk 71 optimal weight: 0.0770 chunk 129 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.3060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.099 12477 Z= 0.177 Angle : 0.621 14.425 16914 Z= 0.325 Chirality : 0.046 0.266 1789 Planarity : 0.005 0.054 2194 Dihedral : 5.565 28.448 1648 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.24 % Favored : 87.76 % Rotamer: Outliers : 2.38 % Allowed : 11.28 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.20), residues: 1503 helix: -1.77 (0.76), residues: 42 sheet: 0.10 (0.26), residues: 409 loop : -2.89 (0.17), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1361 HIS 0.005 0.001 HIS A 318 PHE 0.012 0.001 PHE A 771 TYR 0.019 0.001 TYR A1200 ARG 0.003 0.000 ARG A1177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 1.342 Fit side-chains revert: symmetry clash REVERT: A 400 ARG cc_start: 0.8282 (mtm110) cc_final: 0.7756 (ptm-80) REVERT: A 610 GLU cc_start: 0.7317 (mm-30) cc_final: 0.7113 (mm-30) REVERT: A 645 LYS cc_start: 0.7598 (mttp) cc_final: 0.7122 (mttp) REVERT: A 847 ASN cc_start: 0.7666 (m-40) cc_final: 0.7429 (m-40) REVERT: A 1341 MET cc_start: 0.5461 (tpt) cc_final: 0.5230 (tpt) REVERT: A 1365 TRP cc_start: 0.7027 (m100) cc_final: 0.6805 (m100) REVERT: A 1366 GLU cc_start: 0.8136 (tt0) cc_final: 0.7423 (tp30) outliers start: 32 outliers final: 20 residues processed: 125 average time/residue: 0.2273 time to fit residues: 43.2208 Evaluate side-chains 117 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 845 ASN Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1172 MET Chi-restraints excluded: chain A residue 1450 ASN Chi-restraints excluded: chain A residue 1452 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.0970 chunk 82 optimal weight: 0.0270 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.2240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12477 Z= 0.259 Angle : 0.683 11.756 16914 Z= 0.361 Chirality : 0.048 0.257 1789 Planarity : 0.005 0.061 2194 Dihedral : 5.850 26.563 1648 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.17 % Favored : 86.83 % Rotamer: Outliers : 2.82 % Allowed : 12.84 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.20), residues: 1503 helix: -1.68 (0.76), residues: 48 sheet: 0.01 (0.26), residues: 405 loop : -2.94 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 15 HIS 0.005 0.001 HIS A 318 PHE 0.016 0.002 PHE A 651 TYR 0.019 0.002 TYR A1200 ARG 0.003 0.000 ARG A 918 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 98 time to evaluate : 1.248 Fit side-chains revert: symmetry clash REVERT: A 91 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.8354 (m-80) REVERT: A 400 ARG cc_start: 0.8345 (mtm110) cc_final: 0.7786 (ptm-80) REVERT: A 610 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7168 (mm-30) REVERT: A 645 LYS cc_start: 0.7552 (mttp) cc_final: 0.7343 (mttp) REVERT: A 759 MET cc_start: 0.3184 (mmm) cc_final: 0.0320 (ttt) REVERT: A 847 ASN cc_start: 0.7806 (m-40) cc_final: 0.7578 (m-40) REVERT: A 1341 MET cc_start: 0.5492 (tpt) cc_final: 0.5282 (tpt) REVERT: A 1366 GLU cc_start: 0.8197 (tt0) cc_final: 0.7456 (tp30) outliers start: 38 outliers final: 26 residues processed: 129 average time/residue: 0.2268 time to fit residues: 44.8046 Evaluate side-chains 120 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 967 ASN Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1172 MET Chi-restraints excluded: chain A residue 1215 ASN Chi-restraints excluded: chain A residue 1406 ILE Chi-restraints excluded: chain A residue 1407 THR Chi-restraints excluded: chain A residue 1450 ASN Chi-restraints excluded: chain A residue 1452 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 4.9990 chunk 130 optimal weight: 0.0770 chunk 28 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 67 optimal weight: 20.0000 chunk 12 optimal weight: 0.6980 chunk 76 optimal weight: 0.0570 chunk 139 optimal weight: 0.8980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 12477 Z= 0.172 Angle : 0.628 13.973 16914 Z= 0.330 Chirality : 0.046 0.207 1789 Planarity : 0.005 0.053 2194 Dihedral : 5.668 29.949 1648 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.31 % Favored : 87.69 % Rotamer: Outliers : 2.75 % Allowed : 13.88 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.20), residues: 1503 helix: -1.67 (0.75), residues: 48 sheet: 0.11 (0.26), residues: 410 loop : -2.91 (0.17), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1217 HIS 0.006 0.001 HIS A 318 PHE 0.012 0.001 PHE A 771 TYR 0.019 0.001 TYR A1200 ARG 0.006 0.000 ARG A1308 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 99 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 ARG cc_start: 0.8340 (mtm110) cc_final: 0.7813 (ptm-80) REVERT: A 610 GLU cc_start: 0.7306 (mm-30) cc_final: 0.7082 (mm-30) REVERT: A 759 MET cc_start: 0.2917 (mmm) cc_final: 0.0101 (ttt) REVERT: A 847 ASN cc_start: 0.7686 (m-40) cc_final: 0.7432 (m-40) REVERT: A 1026 HIS cc_start: 0.8068 (t-90) cc_final: 0.7492 (t-90) REVERT: A 1366 GLU cc_start: 0.8209 (tt0) cc_final: 0.7434 (tp30) outliers start: 37 outliers final: 29 residues processed: 128 average time/residue: 0.2108 time to fit residues: 42.1549 Evaluate side-chains 125 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 96 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 967 ASN Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1172 MET Chi-restraints excluded: chain A residue 1215 ASN Chi-restraints excluded: chain A residue 1406 ILE Chi-restraints excluded: chain A residue 1450 ASN Chi-restraints excluded: chain A residue 1452 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12477 Z= 0.201 Angle : 0.644 12.141 16914 Z= 0.340 Chirality : 0.047 0.189 1789 Planarity : 0.005 0.057 2194 Dihedral : 5.706 30.601 1648 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Rotamer: Outliers : 2.52 % Allowed : 14.85 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.78 (0.20), residues: 1503 helix: -1.73 (0.75), residues: 48 sheet: 0.11 (0.26), residues: 417 loop : -2.95 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 15 HIS 0.007 0.001 HIS A 318 PHE 0.014 0.001 PHE A 771 TYR 0.019 0.001 TYR A1200 ARG 0.005 0.000 ARG A1308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 98 time to evaluate : 1.506 Fit side-chains revert: symmetry clash REVERT: A 400 ARG cc_start: 0.8357 (mtm110) cc_final: 0.7803 (ptm-80) REVERT: A 610 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7089 (mm-30) REVERT: A 645 LYS cc_start: 0.7526 (mttp) cc_final: 0.6992 (mttp) REVERT: A 759 MET cc_start: 0.3114 (mmm) cc_final: 0.0348 (ttt) REVERT: A 847 ASN cc_start: 0.7760 (m-40) cc_final: 0.7537 (m-40) REVERT: A 1026 HIS cc_start: 0.8092 (t-90) cc_final: 0.7518 (t-90) REVERT: A 1366 GLU cc_start: 0.8194 (tt0) cc_final: 0.7424 (tp30) outliers start: 34 outliers final: 33 residues processed: 125 average time/residue: 0.2090 time to fit residues: 41.0778 Evaluate side-chains 129 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 96 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 967 ASN Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1172 MET Chi-restraints excluded: chain A residue 1215 ASN Chi-restraints excluded: chain A residue 1406 ILE Chi-restraints excluded: chain A residue 1407 THR Chi-restraints excluded: chain A residue 1450 ASN Chi-restraints excluded: chain A residue 1452 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 98 optimal weight: 0.0570 chunk 71 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12477 Z= 0.177 Angle : 0.627 11.283 16914 Z= 0.331 Chirality : 0.046 0.191 1789 Planarity : 0.005 0.054 2194 Dihedral : 5.641 29.004 1648 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.71 % Favored : 87.29 % Rotamer: Outliers : 2.60 % Allowed : 15.07 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.20), residues: 1503 helix: -1.74 (0.75), residues: 48 sheet: 0.18 (0.26), residues: 404 loop : -2.94 (0.17), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1365 HIS 0.007 0.001 HIS A 318 PHE 0.013 0.001 PHE A 771 TYR 0.020 0.001 TYR A1200 ARG 0.004 0.000 ARG A1308 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 97 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: A 400 ARG cc_start: 0.8352 (mtm110) cc_final: 0.7804 (ptm-80) REVERT: A 610 GLU cc_start: 0.7309 (mm-30) cc_final: 0.7089 (mm-30) REVERT: A 645 LYS cc_start: 0.7520 (mttp) cc_final: 0.6989 (mttp) REVERT: A 759 MET cc_start: 0.3022 (mmm) cc_final: 0.0348 (ttt) REVERT: A 847 ASN cc_start: 0.7701 (m-40) cc_final: 0.7472 (m-40) REVERT: A 1026 HIS cc_start: 0.8131 (t-90) cc_final: 0.7531 (t-90) REVERT: A 1366 GLU cc_start: 0.8214 (tt0) cc_final: 0.7402 (tp30) outliers start: 35 outliers final: 29 residues processed: 125 average time/residue: 0.2100 time to fit residues: 40.8552 Evaluate side-chains 125 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 96 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 967 ASN Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1172 MET Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain A residue 1406 ILE Chi-restraints excluded: chain A residue 1407 THR Chi-restraints excluded: chain A residue 1450 ASN Chi-restraints excluded: chain A residue 1452 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 81 optimal weight: 0.4980 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 127 optimal weight: 0.2980 chunk 88 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12477 Z= 0.200 Angle : 0.645 10.589 16914 Z= 0.340 Chirality : 0.047 0.199 1789 Planarity : 0.005 0.056 2194 Dihedral : 5.720 35.735 1648 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.24 % Favored : 86.69 % Rotamer: Outliers : 2.60 % Allowed : 15.22 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.80 (0.20), residues: 1503 helix: -1.77 (0.74), residues: 48 sheet: 0.12 (0.26), residues: 415 loop : -2.96 (0.17), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1365 HIS 0.008 0.001 HIS A 318 PHE 0.014 0.001 PHE A 771 TYR 0.021 0.001 TYR A1200 ARG 0.003 0.000 ARG A1308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 99 time to evaluate : 1.590 Fit side-chains revert: symmetry clash REVERT: A 135 ASP cc_start: 0.3699 (m-30) cc_final: 0.3441 (t0) REVERT: A 400 ARG cc_start: 0.8363 (mtm110) cc_final: 0.7807 (ptm-80) REVERT: A 610 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7076 (mm-30) REVERT: A 645 LYS cc_start: 0.7509 (mttp) cc_final: 0.6969 (mttp) REVERT: A 759 MET cc_start: 0.2881 (mmm) cc_final: 0.0351 (ttt) REVERT: A 847 ASN cc_start: 0.7739 (m-40) cc_final: 0.7506 (m-40) REVERT: A 1026 HIS cc_start: 0.8120 (t-90) cc_final: 0.7527 (t-90) REVERT: A 1200 TYR cc_start: 0.7165 (t80) cc_final: 0.6816 (t80) REVERT: A 1366 GLU cc_start: 0.8233 (tt0) cc_final: 0.7567 (tp30) outliers start: 35 outliers final: 31 residues processed: 128 average time/residue: 0.2314 time to fit residues: 45.8900 Evaluate side-chains 129 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 98 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 967 ASN Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1172 MET Chi-restraints excluded: chain A residue 1215 ASN Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain A residue 1231 TRP Chi-restraints excluded: chain A residue 1406 ILE Chi-restraints excluded: chain A residue 1450 ASN Chi-restraints excluded: chain A residue 1452 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN A 583 HIS ** A1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12477 Z= 0.392 Angle : 0.810 12.377 16914 Z= 0.430 Chirality : 0.051 0.220 1789 Planarity : 0.006 0.079 2194 Dihedral : 6.432 35.639 1648 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 14.77 % Favored : 85.16 % Rotamer: Outliers : 2.67 % Allowed : 15.14 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.20), residues: 1503 helix: -2.15 (0.69), residues: 48 sheet: -0.24 (0.26), residues: 389 loop : -3.08 (0.16), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 529 HIS 0.009 0.002 HIS A 318 PHE 0.024 0.002 PHE A1461 TYR 0.019 0.002 TYR A 819 ARG 0.004 0.001 ARG A 918 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 104 time to evaluate : 1.390 Fit side-chains revert: symmetry clash REVERT: A 16 SER cc_start: 0.6964 (OUTLIER) cc_final: 0.5799 (t) REVERT: A 91 TYR cc_start: 0.8842 (OUTLIER) cc_final: 0.8103 (m-80) REVERT: A 135 ASP cc_start: 0.4446 (m-30) cc_final: 0.4058 (m-30) REVERT: A 373 ASP cc_start: 0.8231 (p0) cc_final: 0.7760 (p0) REVERT: A 400 ARG cc_start: 0.8396 (mtm110) cc_final: 0.7794 (ptm-80) REVERT: A 645 LYS cc_start: 0.7494 (mttp) cc_final: 0.6891 (mttp) REVERT: A 759 MET cc_start: 0.2916 (mmm) cc_final: 0.0475 (ttt) REVERT: A 847 ASN cc_start: 0.7835 (m-40) cc_final: 0.7388 (m-40) REVERT: A 1143 MET cc_start: 0.8538 (ttp) cc_final: 0.8309 (ttp) REVERT: A 1221 LYS cc_start: 0.7789 (tppt) cc_final: 0.7413 (tptt) REVERT: A 1366 GLU cc_start: 0.8337 (tt0) cc_final: 0.7652 (tp30) outliers start: 36 outliers final: 31 residues processed: 135 average time/residue: 0.2291 time to fit residues: 47.1930 Evaluate side-chains 133 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 100 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 967 ASN Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1172 MET Chi-restraints excluded: chain A residue 1215 ASN Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain A residue 1231 TRP Chi-restraints excluded: chain A residue 1406 ILE Chi-restraints excluded: chain A residue 1450 ASN Chi-restraints excluded: chain A residue 1452 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 15 optimal weight: 0.0040 chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.189904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.142714 restraints weight = 17177.626| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 3.25 r_work: 0.3816 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12477 Z= 0.249 Angle : 0.707 11.540 16914 Z= 0.375 Chirality : 0.049 0.200 1789 Planarity : 0.005 0.069 2194 Dihedral : 6.213 35.347 1648 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.24 % Favored : 86.69 % Rotamer: Outliers : 2.75 % Allowed : 14.92 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.20), residues: 1503 helix: -2.18 (0.69), residues: 48 sheet: -0.25 (0.26), residues: 388 loop : -3.07 (0.16), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 582 HIS 0.009 0.001 HIS A 318 PHE 0.019 0.002 PHE A 651 TYR 0.020 0.002 TYR A1200 ARG 0.003 0.000 ARG A1308 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2699.56 seconds wall clock time: 49 minutes 48.46 seconds (2988.46 seconds total)