Starting phenix.real_space_refine on Fri Oct 23 15:29:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vsw_65309/10_2026/9vsw_65309.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vsw_65309/10_2026/9vsw_65309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vsw_65309/10_2026/9vsw_65309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vsw_65309/10_2026/9vsw_65309.map" model { file = "/net/cci-nas-00/data/ceres_data/9vsw_65309/10_2026/9vsw_65309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vsw_65309/10_2026/9vsw_65309.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.022 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 62 5.16 5 C 6509 2.51 5 N 1654 2.21 5 O 1824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10049 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1252, 9992 Classifications: {'peptide': 1252} Link IDs: {'PTRANS': 53, 'TRANS': 1198} Chain breaks: 5 Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {'VAD': 3} Classifications: {'peptide': 3, 'undetermined': 3} Link IDs: {'TRANS': 3, None: 2} Not linked: pdbres="MEA B 2 " pdbres="VAD B 3 " Not linked: pdbres="MEA B 4 " pdbres="VAD B 5 " Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Planarities with less than four sites: {'VAD:plan-1': 3, 'MEA:plan-2': 3} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 2.38, per 1000 atoms: 0.24 Number of scatterers: 10049 At special positions: 0 Unit cell: (72.148, 100.795, 144.296, 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 62 16.00 O 1824 8.00 N 1654 7.00 C 6509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 712 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A1402 " - pdb=" SG CYS A1444 " distance=2.03 Simple disulfide: pdb=" SG CYS A1418 " - pdb=" SG CYS A1441 " 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 360.5 milliseconds 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2344 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 55.8% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.615A pdb=" N ALA A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 247 through 258 removed outlier: 3.630A pdb=" N PHE A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.841A pdb=" N SER A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 removed outlier: 3.531A pdb=" N SER A 312 " --> pdb=" O ARG A 308 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.821A pdb=" N GLU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 391 through 399 removed outlier: 3.882A pdb=" N PHE A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 415 removed outlier: 3.621A pdb=" N THR A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 444 removed outlier: 4.179A pdb=" N GLU A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 3.587A pdb=" N GLU A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU A 463 " --> pdb=" O PHE A 459 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 511 removed outlier: 3.707A pdb=" N ALA A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 533 removed outlier: 3.727A pdb=" N VAL A 519 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 542 through 559 Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.524A pdb=" N GLU A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.536A pdb=" N LYS A 577 " --> pdb=" O PRO A 573 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS A 580 " --> pdb=" O GLU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 597 removed outlier: 3.594A pdb=" N ALA A 590 " --> pdb=" O PRO A 586 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 591 " --> pdb=" O SER A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 604 Processing helix chain 'A' and resid 604 through 614 removed outlier: 3.739A pdb=" N PHE A 608 " --> pdb=" O MET A 604 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE A 610 " --> pdb=" O MET A 606 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 647 removed outlier: 3.707A pdb=" N THR A 636 " --> pdb=" O CYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 661 Proline residue: A 659 - end of helix Processing helix chain 'A' and resid 662 through 670 Processing helix chain 'A' and resid 676 through 680 Processing helix chain 'A' and resid 684 through 690 removed outlier: 4.052A pdb=" N ASN A 688 " --> pdb=" O SER A 684 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 689 " --> pdb=" O ARG A 685 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 690 " --> pdb=" O TRP A 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 684 through 690' Processing helix chain 'A' and resid 692 through 706 removed outlier: 3.773A pdb=" N VAL A 696 " --> pdb=" O PRO A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 757 through 761 Processing helix chain 'A' and resid 762 through 783 removed outlier: 3.700A pdb=" N GLY A 766 " --> pdb=" O TRP A 762 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 909 removed outlier: 3.624A pdb=" N LEU A 905 " --> pdb=" O LYS A 901 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 906 " --> pdb=" O THR A 902 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 962 removed outlier: 3.691A pdb=" N SER A 959 " --> pdb=" O ALA A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 982 removed outlier: 3.682A pdb=" N ASP A 975 " --> pdb=" O LYS A 971 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP A 982 " --> pdb=" O ASP A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1016 removed outlier: 3.922A pdb=" N GLU A1014 " --> pdb=" O THR A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1049 Processing helix chain 'A' and resid 1062 through 1067 removed outlier: 3.652A pdb=" N ALA A1067 " --> pdb=" O ALA A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1090 No H-bonds generated for 'chain 'A' and resid 1088 through 1090' Processing helix chain 'A' and resid 1091 through 1101 Processing helix chain 'A' and resid 1111 through 1120 removed outlier: 3.577A pdb=" N LEU A1117 " --> pdb=" O ALA A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1137 Processing helix chain 'A' and resid 1139 through 1153 removed outlier: 3.577A pdb=" N GLN A1143 " --> pdb=" O SER A1139 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A1144 " --> pdb=" O SER A1140 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A1148 " --> pdb=" O ALA A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1159 removed outlier: 3.707A pdb=" N LYS A1158 " --> pdb=" O GLU A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1193 Processing helix chain 'A' and resid 1195 through 1215 removed outlier: 3.524A pdb=" N LEU A1203 " --> pdb=" O SER A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1236 removed outlier: 3.603A pdb=" N GLN A1226 " --> pdb=" O MET A1222 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A1236 " --> pdb=" O VAL A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1260 Proline residue: A1248 - end of helix removed outlier: 3.549A pdb=" N LYS A1252 " --> pdb=" O PRO A1248 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A1253 " --> pdb=" O TYR A1249 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A1259 " --> pdb=" O ASP A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1294 removed outlier: 3.948A pdb=" N GLU A1280 " --> pdb=" O GLN A1276 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A1281 " --> pdb=" O ILE A1277 " (cutoff:3.500A) Proline residue: A1282 - end of helix Processing helix chain 'A' and resid 1295 through 1300 Processing helix chain 'A' and resid 1310 through 1339 removed outlier: 3.556A pdb=" N TRP A1319 " --> pdb=" O GLY A1315 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1346 through 1360 removed outlier: 4.329A pdb=" N LEU A1352 " --> pdb=" O ASN A1348 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A1353 " --> pdb=" O LEU A1349 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A1360 " --> pdb=" O MET A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1374 Processing helix chain 'A' and resid 1375 through 1380 Processing helix chain 'A' and resid 1381 through 1395 removed outlier: 4.119A pdb=" N TYR A1385 " --> pdb=" O ASN A1381 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A1393 " --> pdb=" O ALA A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1417 through 1421 removed outlier: 3.729A pdb=" N THR A1420 " --> pdb=" O SER A1417 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1430 removed outlier: 3.519A pdb=" N LYS A1427 " --> pdb=" O ASP A1423 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A1428 " --> pdb=" O PRO A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1448 through 1456 removed outlier: 4.129A pdb=" N PHE A1452 " --> pdb=" O SER A1448 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A1455 " --> pdb=" O THR A1451 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1489 Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 236 removed outlier: 6.196A pdb=" N GLN A 324 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ALA A 359 " --> pdb=" O GLN A 324 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TRP A 326 " --> pdb=" O ALA A 359 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL A 374 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE A 385 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A 376 " --> pdb=" O ILE A 383 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AA4, first strand: chain 'A' and resid 859 through 868 removed outlier: 4.688A pdb=" N PHE A 860 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLY A 883 " --> pdb=" O PHE A 860 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ARG A 862 " --> pdb=" O VAL A 881 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 881 " --> pdb=" O ARG A 862 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU A 864 " --> pdb=" O ASP A 879 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP A 879 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N TYR A 866 " --> pdb=" O ILE A 877 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 937 through 940 removed outlier: 5.885A pdb=" N GLY A 938 " --> pdb=" O PHE A1024 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ASP A1026 " --> pdb=" O GLY A 938 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A 940 " --> pdb=" O ASP A1026 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU A1023 " --> pdb=" O LEU A1055 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N THR A1057 " --> pdb=" O LEU A1023 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU A1025 " --> pdb=" O THR A1057 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR A 891 " --> pdb=" O CYS A1056 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE A 890 " --> pdb=" O ARG A1071 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N LEU A1073 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA A 892 " --> pdb=" O LEU A1073 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU A1075 " --> pdb=" O ALA A 892 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N MET A 894 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU A1072 " --> pdb=" O PHE A1084 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE A1084 " --> pdb=" O LEU A1072 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE A1074 " --> pdb=" O ALA A1082 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1408 through 1410 437 hydrogen bonds defined for protein. 1269 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1675 1.32 - 1.44: 2949 1.44 - 1.57: 5585 1.57 - 1.69: 1 1.69 - 1.81: 101 Bond restraints: 10311 Sorted by residual: bond pdb=" C VAD B 5 " pdb=" N MEA B 6 " ideal model delta sigma weight residual 1.329 1.390 -0.061 1.40e-02 5.10e+03 1.87e+01 bond pdb=" C VAD B 1 " pdb=" N MEA B 2 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.40e-02 5.10e+03 1.71e+01 bond pdb=" C VAD B 3 " pdb=" N MEA B 4 " ideal model delta sigma weight residual 1.329 1.384 -0.055 1.40e-02 5.10e+03 1.52e+01 bond pdb=" N VAL A1119 " pdb=" CA VAL A1119 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.21e+00 bond pdb=" N ILE A 516 " pdb=" CA ILE A 516 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.13e+00 ... (remaining 10306 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 13521 2.11 - 4.21: 389 4.21 - 6.32: 51 6.32 - 8.43: 14 8.43 - 10.54: 6 Bond angle restraints: 13981 Sorted by residual: angle pdb=" N THR A1351 " pdb=" CA THR A1351 " pdb=" CB THR A1351 " ideal model delta sigma weight residual 110.22 116.81 -6.59 1.54e+00 4.22e-01 1.83e+01 angle pdb=" N LEU A1349 " pdb=" CA LEU A1349 " pdb=" C LEU A1349 " ideal model delta sigma weight residual 113.55 108.22 5.33 1.26e+00 6.30e-01 1.79e+01 angle pdb=" OE1 GLN A1284 " pdb=" CD GLN A1284 " pdb=" NE2 GLN A1284 " ideal model delta sigma weight residual 122.60 118.51 4.09 1.00e+00 1.00e+00 1.67e+01 angle pdb=" C LEU A1349 " pdb=" N ALA A1350 " pdb=" CA ALA A1350 " ideal model delta sigma weight residual 120.29 125.99 -5.70 1.42e+00 4.96e-01 1.61e+01 angle pdb=" C SER A 909 " pdb=" N GLU A 910 " pdb=" CA GLU A 910 " ideal model delta sigma weight residual 121.54 128.94 -7.40 1.91e+00 2.74e-01 1.50e+01 ... (remaining 13976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.18: 5345 15.18 - 30.36: 542 30.36 - 45.53: 119 45.53 - 60.71: 18 60.71 - 75.89: 8 Dihedral angle restraints: 6032 sinusoidal: 2371 harmonic: 3661 Sorted by residual: dihedral pdb=" CA VAD B 1 " pdb=" C VAD B 1 " pdb=" N MEA B 2 " pdb=" CA MEA B 2 " ideal model delta harmonic sigma weight residual 180.00 -124.59 -55.41 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" CA VAD B 5 " pdb=" C VAD B 5 " pdb=" N MEA B 6 " pdb=" CA MEA B 6 " ideal model delta harmonic sigma weight residual 180.00 130.23 49.77 0 5.00e+00 4.00e-02 9.91e+01 dihedral pdb=" CB CYS A1418 " pdb=" SG CYS A1418 " pdb=" SG CYS A1441 " pdb=" CB CYS A1441 " ideal model delta sinusoidal sigma weight residual 93.00 142.73 -49.73 1 1.00e+01 1.00e-02 3.39e+01 ... (remaining 6029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1180 0.061 - 0.122: 277 0.122 - 0.183: 40 0.183 - 0.244: 12 0.244 - 0.305: 8 Chirality restraints: 1517 Sorted by residual: chirality pdb=" CB THR A1351 " pdb=" CA THR A1351 " pdb=" OG1 THR A1351 " pdb=" CG2 THR A1351 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA VAL A1119 " pdb=" N VAL A1119 " pdb=" C VAL A1119 " pdb=" CB VAL A1119 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ASN A1348 " pdb=" N ASN A1348 " pdb=" C ASN A1348 " pdb=" CB ASN A1348 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 1514 not shown) Planarity restraints: 1776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB MEA B 2 " 0.099 2.00e-02 2.50e+03 6.22e-02 6.77e+01 pdb=" CG MEA B 2 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 MEA B 2 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 MEA B 2 " -0.063 2.00e-02 2.50e+03 pdb=" CE1 MEA B 2 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 MEA B 2 " 0.030 2.00e-02 2.50e+03 pdb=" CZ MEA B 2 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1328 " 0.061 2.00e-02 2.50e+03 3.54e-02 2.50e+01 pdb=" CG TYR A1328 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A1328 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR A1328 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A1328 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR A1328 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A1328 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR A1328 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1325 " 0.049 2.00e-02 2.50e+03 3.03e-02 1.60e+01 pdb=" CG PHE A1325 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE A1325 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE A1325 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 PHE A1325 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A1325 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A1325 " 0.032 2.00e-02 2.50e+03 ... (remaining 1773 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2310 2.78 - 3.31: 8889 3.31 - 3.84: 17192 3.84 - 4.37: 21633 4.37 - 4.90: 35704 Nonbonded interactions: 85728 Sorted by model distance: nonbonded pdb=" O TYR A 441 " pdb=" OG SER A 445 " model vdw 2.246 3.040 nonbonded pdb=" O ALA A1389 " pdb=" OG1 THR A1393 " model vdw 2.271 3.040 nonbonded pdb=" OD1 ASP A 240 " pdb=" OG SER A 312 " model vdw 2.282 3.040 nonbonded pdb=" OD1 ASP A 334 " pdb=" OG1 THR A 337 " model vdw 2.292 3.040 nonbonded pdb=" O THR A 355 " pdb=" OG1 THR A 355 " model vdw 2.298 3.040 ... (remaining 85723 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.430 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 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 : 0.005 0.061 10317 Z= 0.283 Angle : 0.868 10.535 13987 Z= 0.496 Chirality : 0.058 0.305 1517 Planarity : 0.007 0.074 1776 Dihedral : 12.896 75.891 3679 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.68 % Favored : 95.24 % Rotamer: Outliers : 0.19 % Allowed : 4.68 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.25 (0.17), residues: 1240 helix: -4.22 (0.09), residues: 682 sheet: -2.15 (0.57), residues: 78 loop : -2.20 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1436 TYR 0.061 0.003 TYR A1328 PHE 0.049 0.003 PHE A1325 TRP 0.010 0.001 TRP A 683 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.28 (10311) covalent geometry : angle 0.86782 / 0.50 (13981) SS BOND : bond 0.00301 / 0.15 ( 3) SS BOND : angle 0.65248 / 0.38 ( 6) hydrogen bonds : bond 0.28677 / 18.88 ( 437) hydrogen bonds : angle 10.91342 / 7.48 ( 1269) Misc. bond : bond 0.01704 / 0.85 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 550 MET cc_start: 0.8274 (tpp) cc_final: 0.8053 (tpt) outliers start: 2 outliers final: 2 residues processed: 160 average time/residue: 0.5510 time to fit residues: 94.6700 Evaluate side-chains 108 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 1104 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [108, 49, 97, 113, 53, 5, 33, 123, 65, 62, 51] chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 HIS A 382 GLN A 444 ASN A 538 GLN A 578 HIS A 641 HIS ** A 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 729 ASN A 730 GLN A 758 ASN A 867 GLN A 942 GLN A1059 HIS A1304 ASN A1359 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.108030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.081745 restraints weight = 17629.571| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.91 r_work: 0.2860 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10317 Z= 0.143 Angle : 0.607 8.291 13987 Z= 0.317 Chirality : 0.043 0.199 1517 Planarity : 0.005 0.052 1776 Dihedral : 5.515 67.811 1387 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.59 % Allowed : 10.86 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.21), residues: 1240 helix: -1.91 (0.16), residues: 666 sheet: -1.46 (0.60), residues: 72 loop : -1.67 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 331 TYR 0.016 0.001 TYR A 866 PHE 0.025 0.001 PHE A 517 TRP 0.011 0.001 TRP A 686 HIS 0.003 0.001 HIS A 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (10311) covalent geometry : angle 0.60700 / 0.32 (13981) SS BOND : bond 0.00236 / 0.11 ( 3) SS BOND : angle 0.58371 / 0.36 ( 6) hydrogen bonds : bond 0.04085 / 2.66 ( 437) hydrogen bonds : angle 4.95602 / 3.46 ( 1269) Misc. bond : bond 0.00153 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 174 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: A 334 ASP cc_start: 0.8695 (p0) cc_final: 0.8435 (p0) REVERT: A 361 TYR cc_start: 0.8141 (m-10) cc_final: 0.7914 (m-10) REVERT: A 459 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7185 (m-10) REVERT: A 498 ARG cc_start: 0.8364 (tmt-80) cc_final: 0.7903 (tmm-80) REVERT: A 879 ASP cc_start: 0.8069 (t0) cc_final: 0.7809 (t0) REVERT: A 1004 GLU cc_start: 0.8640 (tt0) cc_final: 0.8437 (tm-30) REVERT: A 1074 PHE cc_start: 0.8873 (t80) cc_final: 0.8589 (t80) REVERT: A 1104 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8008 (p0) REVERT: A 1427 LYS cc_start: 0.9286 (mptt) cc_final: 0.8984 (mmtm) outliers start: 17 outliers final: 3 residues processed: 129 average time/residue: 0.5047 time to fit residues: 70.7534 Evaluate side-chains 98 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1077 LYS Chi-restraints excluded: chain A residue 1104 ASP Chi-restraints excluded: chain A residue 1246 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [84, 123, 1, 103, 116, 37, 78, 104, 0, 109, 7] chunk 84 optimal weight: 5.9990 chunk 123 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 HIS A 714 GLN A1253 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.106213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.079996 restraints weight = 17723.460| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.92 r_work: 0.2839 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10317 Z= 0.152 Angle : 0.577 7.253 13987 Z= 0.298 Chirality : 0.043 0.139 1517 Planarity : 0.004 0.040 1776 Dihedral : 5.000 40.323 1385 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.97 % Allowed : 11.89 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.22), residues: 1240 helix: -0.69 (0.19), residues: 671 sheet: -1.24 (0.57), residues: 82 loop : -1.42 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 331 TYR 0.016 0.001 TYR A1179 PHE 0.020 0.001 PHE A 517 TRP 0.011 0.001 TRP A 686 HIS 0.002 0.001 HIS A 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (10311) covalent geometry : angle 0.57682 / 0.30 (13981) SS BOND : bond 0.00307 / 0.15 ( 3) SS BOND : angle 0.52097 / 0.31 ( 6) hydrogen bonds : bond 0.03780 / 2.46 ( 437) hydrogen bonds : angle 4.40875 / 3.12 ( 1269) Misc. bond : bond 0.00129 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 174 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7621 (m-30) REVERT: A 193 CYS cc_start: 0.8515 (p) cc_final: 0.8183 (m) REVERT: A 299 PHE cc_start: 0.8923 (m-10) cc_final: 0.8693 (m-10) REVERT: A 361 TYR cc_start: 0.8180 (m-10) cc_final: 0.7907 (m-10) REVERT: A 453 LYS cc_start: 0.8912 (ttpp) cc_final: 0.8314 (tptp) REVERT: A 464 ARG cc_start: 0.8450 (tmm-80) cc_final: 0.8085 (tmm-80) REVERT: A 498 ARG cc_start: 0.8303 (tmt-80) cc_final: 0.7815 (tmm-80) REVERT: A 657 MET cc_start: 0.8681 (mmm) cc_final: 0.8425 (mmm) REVERT: A 879 ASP cc_start: 0.8296 (t0) cc_final: 0.7967 (t0) REVERT: A 908 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8842 (mp) REVERT: A 1074 PHE cc_start: 0.8858 (t80) cc_final: 0.8554 (t80) REVERT: A 1104 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.7914 (p0) REVERT: A 1134 GLU cc_start: 0.8641 (mp0) cc_final: 0.8370 (mp0) REVERT: A 1199 SER cc_start: 0.9049 (m) cc_final: 0.8840 (p) REVERT: A 1377 MET cc_start: 0.9054 (tpt) cc_final: 0.8854 (tpt) REVERT: A 1427 LYS cc_start: 0.9321 (mptt) cc_final: 0.9002 (mmtt) outliers start: 21 outliers final: 5 residues processed: 126 average time/residue: 0.5217 time to fit residues: 71.2607 Evaluate side-chains 109 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1104 ASP Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1259 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [91, 4, 94, 22, 8, 26, 106, 62, 20, 80, 12] chunk 91 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 557 ASN ** A 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN A 867 GLN A1035 GLN ** A1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.102760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.077302 restraints weight = 17919.452| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.79 r_work: 0.2786 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10317 Z= 0.220 Angle : 0.612 8.693 13987 Z= 0.315 Chirality : 0.045 0.147 1517 Planarity : 0.004 0.036 1776 Dihedral : 5.033 47.533 1385 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.15 % Allowed : 12.83 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.23), residues: 1240 helix: -0.19 (0.19), residues: 675 sheet: -1.37 (0.59), residues: 72 loop : -1.27 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 331 TYR 0.027 0.002 TYR A 205 PHE 0.019 0.002 PHE A 552 TRP 0.010 0.001 TRP A 686 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.22 (10311) covalent geometry : angle 0.61158 / 0.32 (13981) SS BOND : bond 0.00533 / 0.26 ( 3) SS BOND : angle 0.64688 / 0.37 ( 6) hydrogen bonds : bond 0.03878 / 2.54 ( 437) hydrogen bonds : angle 4.35365 / 3.10 ( 1269) Misc. bond : bond 0.00103 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.299 Fit side-chains REVERT: A 193 CYS cc_start: 0.8501 (p) cc_final: 0.8239 (m) REVERT: A 294 ASN cc_start: 0.8385 (p0) cc_final: 0.8006 (p0) REVERT: A 299 PHE cc_start: 0.8887 (m-10) cc_final: 0.8598 (m-10) REVERT: A 464 ARG cc_start: 0.8554 (tmm-80) cc_final: 0.8235 (tmm-80) REVERT: A 498 ARG cc_start: 0.8278 (tmt-80) cc_final: 0.7810 (tmm-80) REVERT: A 714 GLN cc_start: 0.8160 (tp40) cc_final: 0.7618 (tm-30) REVERT: A 879 ASP cc_start: 0.8439 (t0) cc_final: 0.8065 (t0) REVERT: A 916 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8204 (tp) REVERT: A 1074 PHE cc_start: 0.8937 (t80) cc_final: 0.8593 (t80) REVERT: A 1104 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8013 (p0) REVERT: A 1116 MET cc_start: 0.9099 (ptt) cc_final: 0.8876 (ptp) REVERT: A 1427 LYS cc_start: 0.9406 (mptt) cc_final: 0.9123 (mmtp) outliers start: 23 outliers final: 9 residues processed: 120 average time/residue: 0.5163 time to fit residues: 67.3454 Evaluate side-chains 109 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1104 ASP Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1259 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [20, 47, 84, 67, 9, 121, 38, 15, 100, 57, 3] chunk 20 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 GLN ** A1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.105438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.079500 restraints weight = 17770.041| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.85 r_work: 0.2817 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10317 Z= 0.144 Angle : 0.559 9.534 13987 Z= 0.286 Chirality : 0.043 0.139 1517 Planarity : 0.003 0.037 1776 Dihedral : 4.815 43.961 1385 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.15 % Allowed : 13.30 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.23), residues: 1240 helix: 0.22 (0.20), residues: 675 sheet: -1.35 (0.55), residues: 82 loop : -1.07 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 331 TYR 0.017 0.001 TYR A1179 PHE 0.017 0.001 PHE A 552 TRP 0.010 0.001 TRP A 634 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (10311) covalent geometry : angle 0.55878 / 0.29 (13981) SS BOND : bond 0.00344 / 0.17 ( 3) SS BOND : angle 0.51196 / 0.30 ( 6) hydrogen bonds : bond 0.03382 / 2.21 ( 437) hydrogen bonds : angle 4.10211 / 2.93 ( 1269) Misc. bond : bond 0.00087 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 193 CYS cc_start: 0.8487 (p) cc_final: 0.8229 (m) REVERT: A 294 ASN cc_start: 0.8388 (p0) cc_final: 0.7916 (p0) REVERT: A 299 PHE cc_start: 0.8828 (m-10) cc_final: 0.8501 (m-10) REVERT: A 354 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8584 (p) REVERT: A 361 TYR cc_start: 0.8067 (m-10) cc_final: 0.7835 (m-10) REVERT: A 464 ARG cc_start: 0.8613 (tmm-80) cc_final: 0.8201 (tmm-80) REVERT: A 498 ARG cc_start: 0.8232 (tmt-80) cc_final: 0.7767 (tmm-80) REVERT: A 657 MET cc_start: 0.8643 (mmm) cc_final: 0.8333 (mmm) REVERT: A 714 GLN cc_start: 0.8296 (tp40) cc_final: 0.7717 (tm-30) REVERT: A 879 ASP cc_start: 0.8447 (t0) cc_final: 0.8039 (t0) REVERT: A 916 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8089 (tp) REVERT: A 1074 PHE cc_start: 0.8826 (t80) cc_final: 0.8482 (t80) REVERT: A 1104 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8031 (p0) REVERT: A 1427 LYS cc_start: 0.9384 (mptt) cc_final: 0.9044 (mmtt) outliers start: 23 outliers final: 10 residues processed: 131 average time/residue: 0.4661 time to fit residues: 66.7581 Evaluate side-chains 118 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1104 ASP Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1259 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [62, 85, 63, 114, 11, 32, 30, 83, 94, 49, 22] chunk 62 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 63 optimal weight: 0.0060 chunk 114 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN A1035 GLN A1059 HIS ** A1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1345 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.104804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.078755 restraints weight = 17886.945| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.88 r_work: 0.2803 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10317 Z= 0.168 Angle : 0.578 7.389 13987 Z= 0.297 Chirality : 0.044 0.145 1517 Planarity : 0.003 0.035 1776 Dihedral : 4.747 45.117 1385 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.78 % Allowed : 14.42 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.24), residues: 1240 helix: 0.44 (0.20), residues: 675 sheet: -1.35 (0.54), residues: 82 loop : -1.01 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 331 TYR 0.023 0.001 TYR A 205 PHE 0.018 0.001 PHE A 552 TRP 0.010 0.001 TRP A 686 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (10311) covalent geometry : angle 0.57789 / 0.30 (13981) SS BOND : bond 0.00415 / 0.21 ( 3) SS BOND : angle 0.52810 / 0.30 ( 6) hydrogen bonds : bond 0.03454 / 2.25 ( 437) hydrogen bonds : angle 4.11391 / 2.95 ( 1269) Misc. bond : bond 0.00072 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 294 ASN cc_start: 0.8413 (p0) cc_final: 0.8031 (p0) REVERT: A 299 PHE cc_start: 0.8845 (m-10) cc_final: 0.8526 (m-10) REVERT: A 354 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8644 (p) REVERT: A 357 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8693 (mp) REVERT: A 464 ARG cc_start: 0.8605 (tmm-80) cc_final: 0.8314 (tmm-80) REVERT: A 498 ARG cc_start: 0.8240 (tmt-80) cc_final: 0.7763 (tmm-80) REVERT: A 657 MET cc_start: 0.8677 (mmm) cc_final: 0.8353 (mmm) REVERT: A 714 GLN cc_start: 0.8289 (tp40) cc_final: 0.7750 (tm-30) REVERT: A 879 ASP cc_start: 0.8472 (t0) cc_final: 0.8047 (t0) REVERT: A 916 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8126 (tp) REVERT: A 1074 PHE cc_start: 0.8738 (t80) cc_final: 0.8505 (t80) REVERT: A 1104 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8024 (p0) REVERT: A 1427 LYS cc_start: 0.9374 (mptt) cc_final: 0.9050 (mmtp) outliers start: 19 outliers final: 8 residues processed: 123 average time/residue: 0.4791 time to fit residues: 64.2177 Evaluate side-chains 121 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1104 ASP Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1259 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [6, 116, 65, 53, 111, 122, 71, 93, 36, 0, 87] chunk 6 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 111 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN A1035 GLN A1076 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.105523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.079352 restraints weight = 17731.014| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.90 r_work: 0.2813 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10317 Z= 0.151 Angle : 0.563 7.437 13987 Z= 0.290 Chirality : 0.043 0.140 1517 Planarity : 0.003 0.034 1776 Dihedral : 4.653 43.692 1385 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.78 % Allowed : 14.79 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.24), residues: 1240 helix: 0.69 (0.20), residues: 668 sheet: -1.35 (0.55), residues: 82 loop : -0.96 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 331 TYR 0.020 0.001 TYR A1179 PHE 0.017 0.001 PHE A 552 TRP 0.013 0.001 TRP A 686 HIS 0.003 0.000 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (10311) covalent geometry : angle 0.56349 / 0.29 (13981) SS BOND : bond 0.00366 / 0.18 ( 3) SS BOND : angle 0.47978 / 0.27 ( 6) hydrogen bonds : bond 0.03326 / 2.17 ( 437) hydrogen bonds : angle 4.04688 / 2.91 ( 1269) Misc. bond : bond 0.00064 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 294 ASN cc_start: 0.8426 (p0) cc_final: 0.8010 (p0) REVERT: A 299 PHE cc_start: 0.8844 (m-10) cc_final: 0.8507 (m-10) REVERT: A 357 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8722 (mp) REVERT: A 464 ARG cc_start: 0.8634 (tmm-80) cc_final: 0.8263 (tmm-80) REVERT: A 498 ARG cc_start: 0.8225 (tmt-80) cc_final: 0.7753 (tmm-80) REVERT: A 657 MET cc_start: 0.8699 (mmm) cc_final: 0.8469 (mmm) REVERT: A 714 GLN cc_start: 0.8297 (tp40) cc_final: 0.7750 (tm-30) REVERT: A 879 ASP cc_start: 0.8522 (t0) cc_final: 0.8094 (t0) REVERT: A 916 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8058 (tp) REVERT: A 1074 PHE cc_start: 0.8781 (t80) cc_final: 0.8414 (t80) REVERT: A 1076 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7330 (mp10) REVERT: A 1101 TYR cc_start: 0.8565 (m-80) cc_final: 0.8283 (m-10) REVERT: A 1104 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8314 (m-30) REVERT: A 1427 LYS cc_start: 0.9422 (mptt) cc_final: 0.9081 (mmtm) outliers start: 19 outliers final: 10 residues processed: 131 average time/residue: 0.4782 time to fit residues: 68.4220 Evaluate side-chains 124 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1076 GLN Chi-restraints excluded: chain A residue 1104 ASP Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1259 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [3, 29, 4, 74, 0, 115, 33, 89, 43, 23, 87] chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 HIS A 927 HIS A1035 GLN A1076 GLN ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1450 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.101794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.075748 restraints weight = 17946.650| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.86 r_work: 0.2751 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10317 Z= 0.274 Angle : 0.648 8.002 13987 Z= 0.336 Chirality : 0.047 0.141 1517 Planarity : 0.004 0.032 1776 Dihedral : 4.897 45.356 1385 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.87 % Allowed : 15.92 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.23), residues: 1240 helix: 0.52 (0.19), residues: 678 sheet: -1.25 (0.59), residues: 67 loop : -0.93 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 331 TYR 0.023 0.002 TYR A 205 PHE 0.019 0.002 PHE A 552 TRP 0.015 0.001 TRP A 686 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.27 (10311) covalent geometry : angle 0.64826 / 0.34 (13981) SS BOND : bond 0.00722 / 0.36 ( 3) SS BOND : angle 0.77408 / 0.43 ( 6) hydrogen bonds : bond 0.03941 / 2.58 ( 437) hydrogen bonds : angle 4.35239 / 3.11 ( 1269) Misc. bond : bond 0.00050 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 294 ASN cc_start: 0.8435 (p0) cc_final: 0.8072 (p0) REVERT: A 361 TYR cc_start: 0.7940 (m-10) cc_final: 0.7736 (m-80) REVERT: A 464 ARG cc_start: 0.8643 (tmm-80) cc_final: 0.8323 (tmm-80) REVERT: A 498 ARG cc_start: 0.8186 (tmt-80) cc_final: 0.7747 (tmm-80) REVERT: A 714 GLN cc_start: 0.8280 (tp40) cc_final: 0.7808 (tm-30) REVERT: A 916 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8295 (tp) REVERT: A 1074 PHE cc_start: 0.8864 (t80) cc_final: 0.8506 (t80) REVERT: A 1076 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7241 (mp10) REVERT: A 1101 TYR cc_start: 0.8688 (m-80) cc_final: 0.8372 (m-10) REVERT: A 1427 LYS cc_start: 0.9442 (mptt) cc_final: 0.9055 (mmtm) outliers start: 20 outliers final: 12 residues processed: 116 average time/residue: 0.5183 time to fit residues: 65.3844 Evaluate side-chains 118 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1076 GLN Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1199 SER Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1259 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [15, 25, 88, 32, 14, 114, 82, 4, 55, 6, 111] chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 114 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 55 optimal weight: 0.0670 chunk 6 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 GLN A1076 GLN ** A1253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.106276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.080305 restraints weight = 17690.681| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.89 r_work: 0.2826 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10317 Z= 0.123 Angle : 0.568 11.846 13987 Z= 0.291 Chirality : 0.042 0.139 1517 Planarity : 0.003 0.034 1776 Dihedral : 4.451 20.992 1383 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.50 % Allowed : 16.76 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.24), residues: 1240 helix: 0.86 (0.20), residues: 674 sheet: -1.44 (0.56), residues: 82 loop : -0.86 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 331 TYR 0.022 0.001 TYR A1179 PHE 0.022 0.001 PHE A1373 TRP 0.016 0.001 TRP A 686 HIS 0.002 0.000 HIS A 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (10311) covalent geometry : angle 0.56815 / 0.29 (13981) SS BOND : bond 0.00275 / 0.13 ( 3) SS BOND : angle 0.41459 / 0.24 ( 6) hydrogen bonds : bond 0.03169 / 2.08 ( 437) hydrogen bonds : angle 4.00544 / 2.87 ( 1269) Misc. bond : bond 0.00052 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.380 Fit side-chains REVERT: A 240 ASP cc_start: 0.7696 (t70) cc_final: 0.7272 (t0) REVERT: A 253 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8102 (mp0) REVERT: A 294 ASN cc_start: 0.8416 (p0) cc_final: 0.8071 (p0) REVERT: A 299 PHE cc_start: 0.8917 (m-10) cc_final: 0.8701 (m-10) REVERT: A 464 ARG cc_start: 0.8605 (tmm-80) cc_final: 0.8316 (tmm-80) REVERT: A 498 ARG cc_start: 0.8184 (tmt-80) cc_final: 0.7711 (tmm-80) REVERT: A 714 GLN cc_start: 0.8186 (tp40) cc_final: 0.7667 (tm-30) REVERT: A 879 ASP cc_start: 0.8556 (t0) cc_final: 0.8122 (t0) REVERT: A 916 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8074 (tp) REVERT: A 1074 PHE cc_start: 0.8717 (t80) cc_final: 0.8319 (t80) REVERT: A 1076 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7693 (mp10) REVERT: A 1101 TYR cc_start: 0.8543 (m-80) cc_final: 0.8181 (m-10) REVERT: A 1134 GLU cc_start: 0.8698 (mp0) cc_final: 0.8438 (mp0) REVERT: A 1158 LYS cc_start: 0.8807 (mmpt) cc_final: 0.8470 (mmpt) REVERT: A 1189 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8214 (tm-30) REVERT: A 1427 LYS cc_start: 0.9415 (mptt) cc_final: 0.9023 (mmtm) REVERT: A 1446 MET cc_start: 0.7919 (mtp) cc_final: 0.7164 (ttm) outliers start: 16 outliers final: 6 residues processed: 130 average time/residue: 0.5051 time to fit residues: 71.3808 Evaluate side-chains 117 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1076 GLN Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1259 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [93, 79, 72, 16, 57, 112, 33, 88, 114, 56, 118] chunk 93 optimal weight: 0.9990 chunk 79 optimal weight: 0.0570 chunk 72 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 112 optimal weight: 0.0000 chunk 33 optimal weight: 0.5980 chunk 88 optimal weight: 10.0000 chunk 114 optimal weight: 0.4980 chunk 56 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.4304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 504 ASN ** A 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 GLN A1076 GLN ** A1253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.081190 restraints weight = 17458.533| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.90 r_work: 0.2864 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10317 Z= 0.112 Angle : 0.566 10.390 13987 Z= 0.289 Chirality : 0.042 0.141 1517 Planarity : 0.003 0.035 1776 Dihedral : 4.306 19.754 1383 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.12 % Allowed : 17.70 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.24), residues: 1240 helix: 1.01 (0.20), residues: 671 sheet: -1.30 (0.57), residues: 82 loop : -0.85 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 331 TYR 0.023 0.001 TYR A 205 PHE 0.013 0.001 PHE A1239 TRP 0.018 0.001 TRP A 686 HIS 0.002 0.000 HIS A 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (10311) covalent geometry : angle 0.56610 / 0.29 (13981) SS BOND : bond 0.00195 / 0.10 ( 3) SS BOND : angle 0.41691 / 0.24 ( 6) hydrogen bonds : bond 0.03076 / 2.01 ( 437) hydrogen bonds : angle 3.94069 / 2.82 ( 1269) Misc. bond : bond 0.00043 / 0.02 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.397 Fit side-chains REVERT: A 240 ASP cc_start: 0.7584 (t70) cc_final: 0.7139 (t0) REVERT: A 253 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8095 (mp0) REVERT: A 294 ASN cc_start: 0.8331 (p0) cc_final: 0.7947 (p0) REVERT: A 464 ARG cc_start: 0.8638 (tmm-80) cc_final: 0.8208 (tmm-80) REVERT: A 498 ARG cc_start: 0.8160 (tmt-80) cc_final: 0.7711 (tmm-80) REVERT: A 714 GLN cc_start: 0.8191 (tp40) cc_final: 0.7704 (tm-30) REVERT: A 879 ASP cc_start: 0.8511 (t0) cc_final: 0.8104 (t0) REVERT: A 916 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8109 (tp) REVERT: A 1034 SER cc_start: 0.8987 (t) cc_final: 0.8604 (p) REVERT: A 1074 PHE cc_start: 0.8539 (t80) cc_final: 0.8230 (t80) REVERT: A 1076 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7356 (mp10) REVERT: A 1101 TYR cc_start: 0.8439 (m-80) cc_final: 0.8181 (m-10) REVERT: A 1134 GLU cc_start: 0.8687 (mp0) cc_final: 0.8442 (mp0) REVERT: A 1158 LYS cc_start: 0.8826 (mmpt) cc_final: 0.8528 (mmpt) REVERT: A 1189 GLN cc_start: 0.8435 (tm-30) cc_final: 0.8233 (tm-30) REVERT: A 1356 MET cc_start: 0.8692 (mmm) cc_final: 0.8453 (tpp) REVERT: A 1427 LYS cc_start: 0.9392 (mptt) cc_final: 0.9058 (mmtm) REVERT: A 1446 MET cc_start: 0.7867 (mtp) cc_final: 0.7182 (ttm) outliers start: 12 outliers final: 6 residues processed: 124 average time/residue: 0.4875 time to fit residues: 65.9122 Evaluate side-chains 118 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1076 GLN Chi-restraints excluded: chain A residue 1259 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [122, 90, 50, 3, 25, 60, 63, 72, 36, 106, 69] chunk 122 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 106 optimal weight: 0.0070 chunk 69 optimal weight: 0.8980 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN A1035 GLN A1076 GLN ** A1253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.106009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.079799 restraints weight = 17728.967| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.91 r_work: 0.2820 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10317 Z= 0.143 Angle : 0.582 10.857 13987 Z= 0.298 Chirality : 0.043 0.140 1517 Planarity : 0.003 0.034 1776 Dihedral : 4.331 19.763 1383 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.75 % Allowed : 17.60 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.24), residues: 1240 helix: 1.06 (0.20), residues: 670 sheet: -0.84 (0.63), residues: 72 loop : -0.84 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 331 TYR 0.014 0.001 TYR A1179 PHE 0.019 0.001 PHE A 299 TRP 0.020 0.001 TRP A 686 HIS 0.002 0.000 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (10311) covalent geometry : angle 0.58244 / 0.30 (13981) SS BOND : bond 0.00326 / 0.16 ( 3) SS BOND : angle 0.48104 / 0.27 ( 6) hydrogen bonds : bond 0.03231 / 2.13 ( 437) hydrogen bonds : angle 4.00842 / 2.87 ( 1269) Misc. bond : bond 0.00037 / 0.02 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2529.32 seconds wall clock time: 44 minutes 5.87 seconds (2645.87 seconds total)