Starting phenix.real_space_refine on Thu Sep 26 06:47:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsh_30833/09_2024/7dsh_30833.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsh_30833/09_2024/7dsh_30833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsh_30833/09_2024/7dsh_30833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsh_30833/09_2024/7dsh_30833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsh_30833/09_2024/7dsh_30833.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsh_30833/09_2024/7dsh_30833.cif" } resolution = 3.67 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= 0.002 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 7764 2.51 5 N 2004 2.21 5 O 2242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12071 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1138, 9066 Classifications: {'peptide': 1138} Link IDs: {'PTRANS': 35, 'TRANS': 1102} Chain breaks: 1 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2934 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.24, per 1000 atoms: 0.60 Number of scatterers: 12071 At special positions: 0 Unit cell: (148.755, 108.665, 130.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 57 16.00 P 3 15.00 Mg 1 11.99 O 2242 8.00 N 2004 7.00 C 7764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.03 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=2, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN B 240 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.6 seconds 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2804 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 12 sheets defined 34.3% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 205 through 215 removed outlier: 3.874A pdb=" N LYS A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 Processing helix chain 'A' and resid 239 through 243 removed outlier: 3.671A pdb=" N SER A 243 " --> pdb=" O PRO A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 268 removed outlier: 4.255A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 465 removed outlier: 3.534A pdb=" N ARG A 464 " --> pdb=" O ASP A 461 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 465 " --> pdb=" O ILE A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 461 through 465' Processing helix chain 'A' and resid 549 through 571 removed outlier: 3.807A pdb=" N VAL A 554 " --> pdb=" O ASN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 577 removed outlier: 3.745A pdb=" N ASP A 576 " --> pdb=" O VAL A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 removed outlier: 3.528A pdb=" N TRP A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 605 " --> pdb=" O SER A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 634 removed outlier: 3.657A pdb=" N THR A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 655 removed outlier: 4.120A pdb=" N ILE A 654 " --> pdb=" O SER A 651 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 655 " --> pdb=" O TRP A 652 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 651 through 655' Processing helix chain 'A' and resid 656 through 659 Processing helix chain 'A' and resid 696 through 700 removed outlier: 4.278A pdb=" N GLY A 699 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 726 removed outlier: 3.614A pdb=" N GLU A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 720 " --> pdb=" O LYS A 716 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG A 723 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP A 724 " --> pdb=" O ALA A 720 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 725 " --> pdb=" O LYS A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 775 removed outlier: 3.605A pdb=" N ARG A 765 " --> pdb=" O GLU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 812 removed outlier: 3.807A pdb=" N ALA A 803 " --> pdb=" O PRO A 799 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 804 " --> pdb=" O ASP A 800 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL A 805 " --> pdb=" O GLU A 801 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 903 Processing helix chain 'A' and resid 922 through 936 removed outlier: 3.791A pdb=" N TRP A 926 " --> pdb=" O GLU A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 951 removed outlier: 3.723A pdb=" N SER A 950 " --> pdb=" O VAL A 946 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE A 951 " --> pdb=" O VAL A 947 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 946 through 951' Processing helix chain 'A' and resid 971 through 977 removed outlier: 3.968A pdb=" N GLU A 976 " --> pdb=" O PRO A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1001 Processing helix chain 'A' and resid 1034 through 1044 removed outlier: 3.539A pdb=" N SER A1038 " --> pdb=" O ASP A1034 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A1042 " --> pdb=" O SER A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1079 Processing helix chain 'A' and resid 1087 through 1092 Processing helix chain 'A' and resid 1107 through 1120 removed outlier: 3.560A pdb=" N VAL A1114 " --> pdb=" O LYS A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1139 Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1168 through 1175 Processing helix chain 'A' and resid 1178 through 1183 Processing helix chain 'A' and resid 1183 through 1197 removed outlier: 3.548A pdb=" N ILE A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) Proline residue: A1189 - end of helix removed outlier: 3.567A pdb=" N PHE A1192 " --> pdb=" O ILE A1188 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET A1196 " --> pdb=" O PHE A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1239 removed outlier: 3.847A pdb=" N ILE A1235 " --> pdb=" O SER A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1252 Processing helix chain 'A' and resid 1253 through 1255 No H-bonds generated for 'chain 'A' and resid 1253 through 1255' Processing helix chain 'A' and resid 1256 through 1261 removed outlier: 3.578A pdb=" N LEU A1261 " --> pdb=" O ARG A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1293 removed outlier: 4.046A pdb=" N TRP A1272 " --> pdb=" O ARG A1268 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A1282 " --> pdb=" O LEU A1278 " (cutoff:3.500A) Proline residue: A1288 - end of helix removed outlier: 3.784A pdb=" N VAL A1291 " --> pdb=" O PHE A1287 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A1292 " --> pdb=" O PRO A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1329 removed outlier: 3.653A pdb=" N ILE A1318 " --> pdb=" O TYR A1314 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS A1323 " --> pdb=" O ALA A1319 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A1326 " --> pdb=" O SER A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1347 removed outlier: 3.601A pdb=" N ALA A1343 " --> pdb=" O GLY A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1356 removed outlier: 3.536A pdb=" N THR A1353 " --> pdb=" O VAL A1349 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY A1354 " --> pdb=" O PHE A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1374 removed outlier: 3.861A pdb=" N ARG A1371 " --> pdb=" O LYS A1367 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A1373 " --> pdb=" O ALA A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1375 through 1386 removed outlier: 4.161A pdb=" N TRP A1379 " --> pdb=" O ALA A1375 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A1383 " --> pdb=" O TRP A1379 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A1384 " --> pdb=" O ALA A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1386 through 1404 Proline residue: A1392 - end of helix removed outlier: 4.033A pdb=" N LYS A1401 " --> pdb=" O ASP A1397 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A1403 " --> pdb=" O PHE A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1416 removed outlier: 3.566A pdb=" N GLN A1416 " --> pdb=" O ARG A1412 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 88 through 98 Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.618A pdb=" N VAL B 190 " --> pdb=" O HIS B 186 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 186 through 191' Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 372 through 395 removed outlier: 3.920A pdb=" N TYR B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 409 removed outlier: 3.631A pdb=" N GLY A 520 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 521 " --> pdb=" O ILE A 420 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 447 through 448 removed outlier: 4.102A pdb=" N TYR A 432 " --> pdb=" O ARG A 513 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 485 through 488 removed outlier: 4.146A pdb=" N MET A 485 " --> pdb=" O GLU A 498 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP A 487 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG A 496 " --> pdb=" O TRP A 487 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1099 through 1100 removed outlier: 6.939A pdb=" N LEU A 985 " --> pdb=" O VAL A1100 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU A 662 " --> pdb=" O LYS A 984 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N TRP A 986 " --> pdb=" O GLU A 662 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE A 664 " --> pdb=" O TRP A 986 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 687 through 689 removed outlier: 4.883A pdb=" N LEU A 957 " --> pdb=" O GLN A 915 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLN A 915 " --> pdb=" O LEU A 957 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 781 through 783 removed outlier: 3.555A pdb=" N ASP A 793 " --> pdb=" O GLU A 783 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 813 through 818 removed outlier: 3.655A pdb=" N SER A 814 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE A 824 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 830 " --> pdb=" O MET A 827 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 839 through 840 removed outlier: 3.782A pdb=" N SER A 850 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS A 851 " --> pdb=" O ILE A 869 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 127 through 129 removed outlier: 6.512A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 141 through 144 removed outlier: 3.557A pdb=" N ARG B 143 " --> pdb=" O GLN B 160 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 227 through 228 removed outlier: 6.794A pdb=" N ILE B 227 " --> pdb=" O ALA B 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 246 through 247 327 hydrogen bonds defined for protein. 912 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: 3.70 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1984 1.32 - 1.44: 3402 1.44 - 1.57: 6875 1.57 - 1.69: 6 1.69 - 1.82: 86 Bond restraints: 12353 Sorted by residual: bond pdb=" O3A ACP A1601 " pdb=" PB ACP A1601 " ideal model delta sigma weight residual 1.698 1.599 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" O2B ACP A1601 " pdb=" PB ACP A1601 " ideal model delta sigma weight residual 1.507 1.606 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" N ILE B 214 " pdb=" CA ILE B 214 " ideal model delta sigma weight residual 1.460 1.406 0.054 1.10e-02 8.26e+03 2.40e+01 bond pdb=" C GLU A1028 " pdb=" N PRO A1029 " ideal model delta sigma weight residual 1.337 1.391 -0.054 1.24e-02 6.50e+03 1.92e+01 bond pdb=" C ILE B 214 " pdb=" O ILE B 214 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.03e-02 9.43e+03 1.81e+01 ... (remaining 12348 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 16289 2.75 - 5.49: 382 5.49 - 8.24: 64 8.24 - 10.98: 22 10.98 - 13.73: 4 Bond angle restraints: 16761 Sorted by residual: angle pdb=" C ILE B 214 " pdb=" CA ILE B 214 " pdb=" CB ILE B 214 " ideal model delta sigma weight residual 111.08 103.81 7.27 1.17e+00 7.31e-01 3.86e+01 angle pdb=" N VAL A1311 " pdb=" CA VAL A1311 " pdb=" C VAL A1311 " ideal model delta sigma weight residual 111.81 106.77 5.04 8.60e-01 1.35e+00 3.43e+01 angle pdb=" C MET A1187 " pdb=" N ILE A1188 " pdb=" CA ILE A1188 " ideal model delta sigma weight residual 120.24 123.75 -3.51 6.30e-01 2.52e+00 3.10e+01 angle pdb=" C LYS A 668 " pdb=" N THR A 669 " pdb=" CA THR A 669 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" C CYS A1102 " pdb=" N CYS A1103 " pdb=" CA CYS A1103 " ideal model delta sigma weight residual 123.47 131.75 -8.28 1.53e+00 4.27e-01 2.93e+01 ... (remaining 16756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.24: 7279 35.24 - 70.48: 82 70.48 - 105.72: 13 105.72 - 140.96: 0 140.96 - 176.20: 1 Dihedral angle restraints: 7375 sinusoidal: 3002 harmonic: 4373 Sorted by residual: dihedral pdb=" CA LEU A1101 " pdb=" C LEU A1101 " pdb=" N CYS A1102 " pdb=" CA CYS A1102 " ideal model delta harmonic sigma weight residual -180.00 -136.42 -43.58 0 5.00e+00 4.00e-02 7.60e+01 dihedral pdb=" CB CYS B 110 " pdb=" SG CYS B 110 " pdb=" SG CYS B 159 " pdb=" CB CYS B 159 " ideal model delta sinusoidal sigma weight residual -86.00 -28.45 -57.55 1 1.00e+01 1.00e-02 4.45e+01 dihedral pdb=" CA PHE B 398 " pdb=" C PHE B 398 " pdb=" N GLY B 399 " pdb=" CA GLY B 399 " ideal model delta harmonic sigma weight residual 180.00 148.68 31.32 0 5.00e+00 4.00e-02 3.92e+01 ... (remaining 7372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1399 0.064 - 0.128: 390 0.128 - 0.192: 52 0.192 - 0.256: 18 0.256 - 0.320: 6 Chirality restraints: 1865 Sorted by residual: chirality pdb=" CB ILE A 836 " pdb=" CA ILE A 836 " pdb=" CG1 ILE A 836 " pdb=" CG2 ILE A 836 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA ASN A 675 " pdb=" N ASN A 675 " pdb=" C ASN A 675 " pdb=" CB ASN A 675 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE A1072 " pdb=" CA ILE A1072 " pdb=" CG1 ILE A1072 " pdb=" CG2 ILE A1072 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 1862 not shown) Planarity restraints: 2124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A1408 " 0.031 2.00e-02 2.50e+03 5.98e-02 3.58e+01 pdb=" C VAL A1408 " -0.104 2.00e-02 2.50e+03 pdb=" O VAL A1408 " 0.038 2.00e-02 2.50e+03 pdb=" N GLU A1409 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 398 " 0.029 2.00e-02 2.50e+03 5.71e-02 3.26e+01 pdb=" C PHE B 398 " -0.099 2.00e-02 2.50e+03 pdb=" O PHE B 398 " 0.037 2.00e-02 2.50e+03 pdb=" N GLY B 399 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 986 " -0.023 2.00e-02 2.50e+03 2.07e-02 1.07e+01 pdb=" CG TRP A 986 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 986 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 986 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 986 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP A 986 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 986 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 986 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 986 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 986 " -0.006 2.00e-02 2.50e+03 ... (remaining 2121 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 223 2.66 - 3.22: 10909 3.22 - 3.78: 18638 3.78 - 4.34: 25981 4.34 - 4.90: 41468 Nonbonded interactions: 97219 Sorted by model distance: nonbonded pdb=" NE2 HIS B 209 " pdb=" OG SER B 220 " model vdw 2.099 3.120 nonbonded pdb=" N ASP B 210 " pdb=" OD1 ASP B 210 " model vdw 2.215 3.120 nonbonded pdb=" OH TYR A1193 " pdb=" OE1 GLN A1280 " model vdw 2.243 3.040 nonbonded pdb=" O THR A1353 " pdb=" OG SER A1357 " model vdw 2.250 3.040 nonbonded pdb=" O3G ACP A1601 " pdb="MG MG A1602 " model vdw 2.254 2.170 ... (remaining 97214 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.050 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 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 : 0.007 0.099 12353 Z= 0.408 Angle : 1.085 13.725 16761 Z= 0.585 Chirality : 0.063 0.320 1865 Planarity : 0.007 0.070 2123 Dihedral : 12.541 176.197 4565 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.50 % Favored : 90.36 % Rotamer: Outliers : 0.46 % Allowed : 3.61 % Favored : 95.93 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -6.04 (0.14), residues: 1494 helix: -4.69 (0.09), residues: 536 sheet: -3.88 (0.36), residues: 128 loop : -3.64 (0.16), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP B 308 HIS 0.013 0.002 HIS A 216 PHE 0.030 0.003 PHE A1287 TYR 0.030 0.003 TYR A1217 ARG 0.006 0.001 ARG B 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 191 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ASN cc_start: 0.7842 (t0) cc_final: 0.7468 (t0) REVERT: A 740 TYR cc_start: 0.6855 (p90) cc_final: 0.6138 (p90) REVERT: A 945 GLU cc_start: 0.7323 (tt0) cc_final: 0.6957 (tt0) REVERT: A 1097 CYS cc_start: 0.7329 (p) cc_final: 0.7069 (p) REVERT: A 1139 GLN cc_start: 0.6897 (mt0) cc_final: 0.6677 (pt0) REVERT: A 1296 MET cc_start: 0.8377 (mmm) cc_final: 0.8060 (mmt) REVERT: A 1306 ASP cc_start: 0.7188 (p0) cc_final: 0.6944 (t0) REVERT: A 1321 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7448 (mp) outliers start: 6 outliers final: 3 residues processed: 197 average time/residue: 0.2619 time to fit residues: 72.6366 Evaluate side-chains 110 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain B residue 212 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 71 optimal weight: 0.0470 chunk 86 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS A 475 HIS A 484 ASN A 550 ASN A 736 ASN A 778 HIS A 831 GLN A1139 GLN A1307 HIS B 155 GLN B 172 ASN B 256 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12353 Z= 0.212 Angle : 0.706 10.285 16761 Z= 0.370 Chirality : 0.047 0.207 1865 Planarity : 0.005 0.046 2123 Dihedral : 10.516 174.331 1738 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 1.92 % Allowed : 7.14 % Favored : 90.94 % 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: -4.83 (0.17), residues: 1494 helix: -3.13 (0.17), residues: 541 sheet: -3.46 (0.36), residues: 144 loop : -3.28 (0.18), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 308 HIS 0.004 0.001 HIS A 899 PHE 0.038 0.002 PHE A 679 TYR 0.022 0.002 TYR A1040 ARG 0.008 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.4609 (pttm) cc_final: 0.4398 (mtpt) REVERT: A 477 ASN cc_start: 0.7648 (t0) cc_final: 0.7110 (t0) REVERT: A 482 GLN cc_start: 0.6554 (pm20) cc_final: 0.6159 (mp10) REVERT: A 740 TYR cc_start: 0.6661 (p90) cc_final: 0.6337 (p90) REVERT: A 827 MET cc_start: 0.8388 (ppp) cc_final: 0.8121 (ppp) REVERT: A 942 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7989 (t0) REVERT: A 1006 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8189 (pp) REVERT: B 84 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8409 (p) outliers start: 25 outliers final: 14 residues processed: 130 average time/residue: 0.2311 time to fit residues: 44.9232 Evaluate side-chains 108 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 942 ASP Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1223 MET Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 112 optimal weight: 0.4980 chunk 92 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 660 GLN A 704 GLN A 927 ASN A 998 ASN A1139 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12353 Z= 0.205 Angle : 0.647 7.793 16761 Z= 0.338 Chirality : 0.045 0.194 1865 Planarity : 0.004 0.042 2123 Dihedral : 9.393 174.599 1735 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.61 % Allowed : 9.45 % Favored : 87.94 % 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: -4.05 (0.19), residues: 1494 helix: -2.14 (0.20), residues: 530 sheet: -3.18 (0.38), residues: 145 loop : -3.06 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 308 HIS 0.005 0.001 HIS A 899 PHE 0.018 0.002 PHE A 679 TYR 0.025 0.002 TYR A1040 ARG 0.004 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 98 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7450 (tp) REVERT: A 267 VAL cc_start: 0.7371 (OUTLIER) cc_final: 0.7099 (t) REVERT: A 477 ASN cc_start: 0.7645 (t0) cc_final: 0.7114 (t0) REVERT: A 482 GLN cc_start: 0.6505 (pm20) cc_final: 0.6180 (mp10) REVERT: A 804 LEU cc_start: 0.7963 (mm) cc_final: 0.7658 (mm) REVERT: A 827 MET cc_start: 0.8412 (ppp) cc_final: 0.8113 (ppp) REVERT: A 852 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.6812 (mt) REVERT: A 942 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8157 (t0) REVERT: A 1124 MET cc_start: 0.6976 (mmt) cc_final: 0.6772 (mmt) REVERT: A 1306 ASP cc_start: 0.6898 (OUTLIER) cc_final: 0.6589 (p0) outliers start: 34 outliers final: 19 residues processed: 124 average time/residue: 0.2400 time to fit residues: 45.7836 Evaluate side-chains 110 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 942 ASP Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 0.2980 chunk 101 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 64 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 0.2980 chunk 144 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 38 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12353 Z= 0.170 Angle : 0.608 7.517 16761 Z= 0.316 Chirality : 0.045 0.180 1865 Planarity : 0.003 0.041 2123 Dihedral : 8.773 175.336 1735 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.15 % Allowed : 9.60 % Favored : 87.25 % 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: -3.59 (0.20), residues: 1494 helix: -1.62 (0.21), residues: 527 sheet: -2.93 (0.40), residues: 145 loop : -2.89 (0.19), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 517 HIS 0.005 0.001 HIS A 899 PHE 0.019 0.001 PHE A1399 TYR 0.025 0.001 TYR A1040 ARG 0.003 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 102 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: A 224 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7511 (tp) REVERT: A 267 VAL cc_start: 0.7381 (OUTLIER) cc_final: 0.7080 (t) REVERT: A 477 ASN cc_start: 0.7622 (t0) cc_final: 0.7053 (t0) REVERT: A 482 GLN cc_start: 0.6388 (pm20) cc_final: 0.6108 (mp10) REVERT: A 827 MET cc_start: 0.8358 (ppp) cc_final: 0.8046 (ppp) REVERT: A 852 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6790 (mt) REVERT: A 1109 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7236 (mp-120) REVERT: A 1196 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.6707 (ppp) REVERT: A 1306 ASP cc_start: 0.6721 (OUTLIER) cc_final: 0.6394 (p0) outliers start: 41 outliers final: 22 residues processed: 133 average time/residue: 0.2142 time to fit residues: 44.2119 Evaluate side-chains 115 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 87 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 129 optimal weight: 0.4980 chunk 36 optimal weight: 0.0270 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12353 Z= 0.184 Angle : 0.608 8.449 16761 Z= 0.314 Chirality : 0.044 0.180 1865 Planarity : 0.003 0.041 2123 Dihedral : 8.425 175.113 1733 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.23 % Allowed : 10.45 % Favored : 86.33 % 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: -3.32 (0.20), residues: 1494 helix: -1.33 (0.22), residues: 527 sheet: -2.64 (0.42), residues: 133 loop : -2.82 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 348 HIS 0.005 0.001 HIS A 899 PHE 0.019 0.001 PHE A1399 TYR 0.022 0.001 TYR A1040 ARG 0.002 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 94 time to evaluate : 1.367 Fit side-chains revert: symmetry clash REVERT: A 224 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7628 (tp) REVERT: A 267 VAL cc_start: 0.7450 (OUTLIER) cc_final: 0.7162 (t) REVERT: A 477 ASN cc_start: 0.7588 (t0) cc_final: 0.6979 (t0) REVERT: A 482 GLN cc_start: 0.6250 (pm20) cc_final: 0.5940 (mp10) REVERT: A 827 MET cc_start: 0.8243 (ppp) cc_final: 0.7958 (ppp) REVERT: A 852 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.6873 (mt) REVERT: A 1109 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7320 (mp-120) REVERT: A 1196 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.6818 (ppp) REVERT: A 1306 ASP cc_start: 0.6685 (OUTLIER) cc_final: 0.6339 (p0) REVERT: B 56 ASP cc_start: 0.6788 (t70) cc_final: 0.6567 (t0) outliers start: 42 outliers final: 25 residues processed: 127 average time/residue: 0.2113 time to fit residues: 41.9646 Evaluate side-chains 119 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 88 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 10.0000 chunk 129 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12353 Z= 0.238 Angle : 0.640 8.650 16761 Z= 0.328 Chirality : 0.046 0.185 1865 Planarity : 0.003 0.040 2123 Dihedral : 8.461 176.799 1733 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.38 % Allowed : 11.37 % Favored : 85.25 % 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: -3.23 (0.20), residues: 1494 helix: -1.19 (0.22), residues: 530 sheet: -2.70 (0.42), residues: 146 loop : -2.77 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 986 HIS 0.005 0.001 HIS A 899 PHE 0.018 0.002 PHE A1399 TYR 0.022 0.002 TYR A1040 ARG 0.003 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 97 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 PRO cc_start: 0.8176 (Cg_exo) cc_final: 0.7928 (Cg_endo) REVERT: A 267 VAL cc_start: 0.7509 (OUTLIER) cc_final: 0.7202 (t) REVERT: A 477 ASN cc_start: 0.7568 (t0) cc_final: 0.6955 (t0) REVERT: A 482 GLN cc_start: 0.6253 (pm20) cc_final: 0.5933 (mp10) REVERT: A 827 MET cc_start: 0.8285 (ppp) cc_final: 0.7953 (ppp) REVERT: A 849 MET cc_start: 0.5168 (tpt) cc_final: 0.4857 (tpt) REVERT: A 852 ILE cc_start: 0.7276 (OUTLIER) cc_final: 0.6806 (mt) REVERT: A 1109 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7277 (mp-120) REVERT: A 1196 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.6847 (ppp) REVERT: A 1306 ASP cc_start: 0.6716 (OUTLIER) cc_final: 0.6415 (p0) REVERT: B 127 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.7126 (mp10) outliers start: 44 outliers final: 34 residues processed: 132 average time/residue: 0.2243 time to fit residues: 44.4393 Evaluate side-chains 127 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 87 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12353 Z= 0.192 Angle : 0.613 8.899 16761 Z= 0.314 Chirality : 0.044 0.180 1865 Planarity : 0.003 0.040 2123 Dihedral : 8.313 177.700 1733 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 3.69 % Allowed : 11.52 % Favored : 84.79 % 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: -3.05 (0.21), residues: 1494 helix: -0.99 (0.23), residues: 526 sheet: -2.64 (0.43), residues: 136 loop : -2.71 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 986 HIS 0.005 0.001 HIS A 899 PHE 0.016 0.001 PHE A1399 TYR 0.021 0.001 TYR A1040 ARG 0.006 0.000 ARG A 703 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 96 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 PRO cc_start: 0.7992 (Cg_exo) cc_final: 0.7749 (Cg_endo) REVERT: A 267 VAL cc_start: 0.7459 (OUTLIER) cc_final: 0.7157 (t) REVERT: A 477 ASN cc_start: 0.7548 (t0) cc_final: 0.6945 (t0) REVERT: A 482 GLN cc_start: 0.6335 (pm20) cc_final: 0.6079 (mp10) REVERT: A 523 MET cc_start: -0.1006 (OUTLIER) cc_final: -0.1262 (ptt) REVERT: A 679 PHE cc_start: 0.7127 (t80) cc_final: 0.6871 (t80) REVERT: A 827 MET cc_start: 0.8290 (ppp) cc_final: 0.7945 (ppp) REVERT: A 849 MET cc_start: 0.5255 (tpt) cc_final: 0.4967 (tpt) REVERT: A 852 ILE cc_start: 0.7281 (OUTLIER) cc_final: 0.6904 (mt) REVERT: A 1109 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7314 (mp-120) REVERT: A 1196 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.6794 (ppp) REVERT: A 1306 ASP cc_start: 0.6622 (OUTLIER) cc_final: 0.6293 (p0) REVERT: B 127 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7103 (mp10) outliers start: 48 outliers final: 36 residues processed: 133 average time/residue: 0.2212 time to fit residues: 45.2567 Evaluate side-chains 133 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 90 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 0.0070 chunk 57 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12353 Z= 0.291 Angle : 0.675 9.713 16761 Z= 0.344 Chirality : 0.047 0.199 1865 Planarity : 0.004 0.038 2123 Dihedral : 8.491 179.060 1733 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 3.99 % Allowed : 11.60 % Favored : 84.41 % 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: -3.13 (0.21), residues: 1494 helix: -1.12 (0.22), residues: 539 sheet: -2.79 (0.42), residues: 147 loop : -2.69 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 986 HIS 0.004 0.001 HIS A 899 PHE 0.018 0.002 PHE A1366 TYR 0.020 0.002 TYR A 740 ARG 0.006 0.000 ARG A 703 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 92 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 PRO cc_start: 0.8011 (Cg_exo) cc_final: 0.7766 (Cg_endo) REVERT: A 267 VAL cc_start: 0.7590 (OUTLIER) cc_final: 0.7273 (t) REVERT: A 477 ASN cc_start: 0.7575 (t0) cc_final: 0.6926 (t0) REVERT: A 482 GLN cc_start: 0.6326 (pm20) cc_final: 0.6004 (mp10) REVERT: A 827 MET cc_start: 0.8232 (ppp) cc_final: 0.7993 (ppp) REVERT: A 849 MET cc_start: 0.5397 (tpt) cc_final: 0.5120 (tpt) REVERT: A 852 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.6971 (mt) REVERT: A 1109 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7214 (mp-120) REVERT: A 1306 ASP cc_start: 0.6745 (OUTLIER) cc_final: 0.6474 (p0) REVERT: B 127 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.7089 (mp10) outliers start: 52 outliers final: 38 residues processed: 133 average time/residue: 0.2110 time to fit residues: 42.9126 Evaluate side-chains 130 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 87 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 0.5980 chunk 137 optimal weight: 0.0020 chunk 125 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12353 Z= 0.187 Angle : 0.616 9.614 16761 Z= 0.313 Chirality : 0.044 0.184 1865 Planarity : 0.003 0.041 2123 Dihedral : 8.276 179.002 1733 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.00 % Allowed : 12.90 % Favored : 84.10 % 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: -2.91 (0.21), residues: 1494 helix: -0.91 (0.22), residues: 542 sheet: -2.69 (0.42), residues: 147 loop : -2.57 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 517 HIS 0.005 0.001 HIS A 899 PHE 0.015 0.001 PHE A1399 TYR 0.021 0.001 TYR A1040 ARG 0.004 0.000 ARG A 703 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 92 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 VAL cc_start: 0.7627 (OUTLIER) cc_final: 0.7303 (t) REVERT: A 477 ASN cc_start: 0.7491 (t0) cc_final: 0.6862 (t0) REVERT: A 482 GLN cc_start: 0.6353 (pm20) cc_final: 0.6071 (mp10) REVERT: A 827 MET cc_start: 0.8223 (ppp) cc_final: 0.7861 (ppp) REVERT: A 849 MET cc_start: 0.5320 (tpt) cc_final: 0.5054 (tpt) REVERT: A 1109 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7364 (mp-120) REVERT: A 1306 ASP cc_start: 0.6581 (OUTLIER) cc_final: 0.6272 (p0) REVERT: B 127 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.7139 (mp10) outliers start: 39 outliers final: 31 residues processed: 121 average time/residue: 0.2289 time to fit residues: 41.6576 Evaluate side-chains 122 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 87 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 67 optimal weight: 0.0770 chunk 98 optimal weight: 0.6980 chunk 148 optimal weight: 8.9990 chunk 136 optimal weight: 0.0000 chunk 118 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12353 Z= 0.164 Angle : 0.614 9.388 16761 Z= 0.311 Chirality : 0.044 0.176 1865 Planarity : 0.003 0.042 2123 Dihedral : 8.126 177.819 1733 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 2.92 % Allowed : 13.21 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.21), residues: 1494 helix: -0.77 (0.23), residues: 534 sheet: -2.52 (0.44), residues: 136 loop : -2.59 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 517 HIS 0.003 0.001 HIS A 899 PHE 0.014 0.001 PHE A1399 TYR 0.021 0.001 TYR A1040 ARG 0.006 0.000 ARG A 714 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 96 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 VAL cc_start: 0.7612 (OUTLIER) cc_final: 0.7276 (t) REVERT: A 477 ASN cc_start: 0.7449 (t0) cc_final: 0.6798 (t0) REVERT: A 771 MET cc_start: 0.7799 (mmt) cc_final: 0.7452 (mmt) REVERT: A 827 MET cc_start: 0.8228 (ppp) cc_final: 0.7858 (ppp) REVERT: A 849 MET cc_start: 0.5194 (tpt) cc_final: 0.4964 (tpt) REVERT: A 1109 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7333 (mp-120) REVERT: A 1196 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6795 (ppp) REVERT: A 1306 ASP cc_start: 0.6503 (OUTLIER) cc_final: 0.6172 (p0) REVERT: B 127 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7112 (mp10) outliers start: 38 outliers final: 31 residues processed: 126 average time/residue: 0.2222 time to fit residues: 42.5043 Evaluate side-chains 123 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 87 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 14 optimal weight: 0.0570 chunk 21 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 overall best weight: 0.7698 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.131741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.098071 restraints weight = 20228.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.095563 restraints weight = 20579.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.096656 restraints weight = 17047.475| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12353 Z= 0.201 Angle : 0.618 9.207 16761 Z= 0.314 Chirality : 0.045 0.173 1865 Planarity : 0.003 0.042 2123 Dihedral : 8.102 177.479 1733 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.84 % Allowed : 13.21 % Favored : 83.95 % 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: -2.75 (0.21), residues: 1494 helix: -0.68 (0.23), residues: 527 sheet: -2.59 (0.45), residues: 126 loop : -2.57 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 517 HIS 0.003 0.001 HIS A 899 PHE 0.013 0.001 PHE A1285 TYR 0.020 0.002 TYR A1040 ARG 0.005 0.000 ARG A1087 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2258.84 seconds wall clock time: 45 minutes 50.77 seconds (2750.77 seconds total)