Starting phenix.real_space_refine on Sun Sep 29 04:53:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p03_13142/09_2024/7p03_13142.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p03_13142/09_2024/7p03_13142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p03_13142/09_2024/7p03_13142.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p03_13142/09_2024/7p03_13142.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p03_13142/09_2024/7p03_13142.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p03_13142/09_2024/7p03_13142.cif" } resolution = 3.45 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= 0.001 sd= 0.159 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: 5 Type Number sf(0) Gaussians S 67 5.16 5 C 6900 2.51 5 N 1754 2.21 5 O 1930 1.98 5 H 10498 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 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: 21149 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 21149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1333, 21149 Classifications: {'peptide': 1333} Link IDs: {'PTRANS': 51, 'TRANS': 1281} Chain breaks: 5 Time building chain proxies: 9.96, per 1000 atoms: 0.47 Number of scatterers: 21149 At special positions: 0 Unit cell: (80.52, 106.14, 152.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 O 1930 8.00 N 1754 7.00 C 6900 6.00 H 10498 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1411 " - pdb=" SG CYS A1455 " 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=0, symmetry=0 Time building additional restraints: 5.80 Conformation dependent library (CDL) restraints added in 1.6 seconds 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2498 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 6 sheets defined 62.2% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 36 through 54 Processing helix chain 'A' and resid 103 through 117 Processing helix chain 'A' and resid 151 through 165 Processing helix chain 'A' and resid 198 through 207 removed outlier: 3.516A pdb=" N SER A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.628A pdb=" N LYS A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 removed outlier: 3.937A pdb=" N THR A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 261 " --> pdb=" O THR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 291 removed outlier: 4.036A pdb=" N TYR A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 325 removed outlier: 3.581A pdb=" N SER A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 358 removed outlier: 3.682A pdb=" N LEU A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 Processing helix chain 'A' and resid 396 through 405 removed outlier: 3.703A pdb=" N GLY A 405 " --> pdb=" O PHE A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 422 through 427 removed outlier: 6.845A pdb=" N SER A 425 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 427 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 Processing helix chain 'A' and resid 443 through 454 Processing helix chain 'A' and resid 454 through 469 removed outlier: 3.918A pdb=" N LYS A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 519 Processing helix chain 'A' and resid 519 through 540 removed outlier: 4.234A pdb=" N THR A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 542 No H-bonds generated for 'chain 'A' and resid 541 through 542' Processing helix chain 'A' and resid 543 through 548 removed outlier: 3.541A pdb=" N LYS A 547 " --> pdb=" O ILE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 569 removed outlier: 3.742A pdb=" N MET A 560 " --> pdb=" O ARG A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 574 removed outlier: 4.820A pdb=" N LEU A 573 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 591 removed outlier: 3.578A pdb=" N ALA A 581 " --> pdb=" O SER A 577 " (cutoff:3.500A) Proline residue: A 583 - end of helix Processing helix chain 'A' and resid 595 through 607 removed outlier: 3.844A pdb=" N GLU A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 627 removed outlier: 4.159A pdb=" N VAL A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN A 619 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP A 627 " --> pdb=" O TYR A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 660 removed outlier: 4.450A pdb=" N PHE A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS A 655 " --> pdb=" O HIS A 651 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR A 660 " --> pdb=" O VAL A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 680 removed outlier: 4.823A pdb=" N VAL A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) Proline residue: A 669 - end of helix Processing helix chain 'A' and resid 686 through 690 removed outlier: 3.606A pdb=" N ILE A 690 " --> pdb=" O LYS A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 693 No H-bonds generated for 'chain 'A' and resid 691 through 693' Processing helix chain 'A' and resid 694 through 700 removed outlier: 3.669A pdb=" N TRP A 698 " --> pdb=" O SER A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 716 removed outlier: 3.624A pdb=" N TYR A 705 " --> pdb=" O ASN A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 733 Processing helix chain 'A' and resid 736 through 740 removed outlier: 3.846A pdb=" N SER A 740 " --> pdb=" O SER A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 764 Processing helix chain 'A' and resid 767 through 771 Processing helix chain 'A' and resid 772 through 796 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.564A pdb=" N LEU A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 945 Processing helix chain 'A' and resid 960 through 973 removed outlier: 3.588A pdb=" N SER A 968 " --> pdb=" O SER A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 993 removed outlier: 3.868A pdb=" N ASN A 983 " --> pdb=" O ILE A 979 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 984 " --> pdb=" O GLU A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1025 removed outlier: 3.808A pdb=" N GLU A1023 " --> pdb=" O THR A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1060 removed outlier: 3.514A pdb=" N GLY A1060 " --> pdb=" O LEU A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1076 removed outlier: 4.040A pdb=" N GLN A1076 " --> pdb=" O ALA A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1100 through 1110 Processing helix chain 'A' and resid 1120 through 1129 removed outlier: 4.125A pdb=" N LEU A1126 " --> pdb=" O ALA A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1148 removed outlier: 3.758A pdb=" N VAL A1144 " --> pdb=" O ASP A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1162 removed outlier: 3.652A pdb=" N ARG A1152 " --> pdb=" O SER A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1200 Processing helix chain 'A' and resid 1202 through 1224 removed outlier: 3.500A pdb=" N LEU A1206 " --> pdb=" O SER A1202 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A1212 " --> pdb=" O SER A1208 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A1218 " --> pdb=" O ILE A1214 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A1224 " --> pdb=" O ILE A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1244 Processing helix chain 'A' and resid 1247 through 1270 Proline residue: A1257 - end of helix Processing helix chain 'A' and resid 1277 through 1306 removed outlier: 3.639A pdb=" N VAL A1290 " --> pdb=" O ILE A1286 " (cutoff:3.500A) Proline residue: A1291 - end of helix removed outlier: 3.720A pdb=" N LEU A1295 " --> pdb=" O PRO A1291 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR A1306 " --> pdb=" O PHE A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1318 removed outlier: 3.559A pdb=" N ASN A1313 " --> pdb=" O GLY A1309 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A1317 " --> pdb=" O ASN A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1348 removed outlier: 3.879A pdb=" N PHE A1327 " --> pdb=" O ARG A1323 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR A1335 " --> pdb=" O SER A1331 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A1346 " --> pdb=" O GLY A1342 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE A1348 " --> pdb=" O LEU A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1369 removed outlier: 3.646A pdb=" N ALA A1355 " --> pdb=" O VAL A1351 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A1369 " --> pdb=" O MET A1365 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1390 Processing helix chain 'A' and resid 1390 through 1405 removed outlier: 4.513A pdb=" N TYR A1394 " --> pdb=" O SER A1390 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1432 Processing helix chain 'A' and resid 1433 through 1438 Processing helix chain 'A' and resid 1459 through 1468 removed outlier: 3.666A pdb=" N TYR A1463 " --> pdb=" O THR A1459 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A1465 " --> pdb=" O ASN A1461 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN A1466 " --> pdb=" O ASP A1462 " (cutoff:3.500A) Processing helix chain 'A' and resid 1470 through 1472 No H-bonds generated for 'chain 'A' and resid 1470 through 1472' Processing helix chain 'A' and resid 1473 through 1500 removed outlier: 3.820A pdb=" N ASN A1477 " --> pdb=" O GLU A1473 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 183 removed outlier: 5.004A pdb=" N PHE A 173 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ALA A 139 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE A 175 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER A 137 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LYS A 177 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N SER A 135 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N MET A 179 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 183 removed outlier: 5.004A pdb=" N PHE A 173 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ALA A 139 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE A 175 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER A 137 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LYS A 177 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N SER A 135 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N MET A 179 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 226 " --> pdb=" O TYR A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 362 through 364 removed outlier: 6.306A pdb=" N LEU A 189 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 392 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR A 390 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASP A 384 " --> pdb=" O GLN A 388 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLN A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 719 through 721 Processing sheet with id=AA5, first strand: chain 'A' and resid 926 through 932 removed outlier: 7.208A pdb=" N VAL A 926 " --> pdb=" O TYR A 876 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR A 876 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR A 928 " --> pdb=" O LEU A 874 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU A 874 " --> pdb=" O THR A 928 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP A 930 " --> pdb=" O ARG A 872 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG A 872 " --> pdb=" O ASP A 930 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N VAL A 891 " --> pdb=" O ASN A 873 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N CYS A 875 " --> pdb=" O ASN A 889 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN A 889 " --> pdb=" O CYS A 875 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N GLU A 877 " --> pdb=" O ILE A 887 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 887 " --> pdb=" O GLU A 877 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N THR A1090 " --> pdb=" O ASN A 889 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL A 891 " --> pdb=" O THR A1090 " (cutoff:3.500A) removed outlier: 11.676A pdb=" N TYR A1092 " --> pdb=" O VAL A 891 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N GLY A 893 " --> pdb=" O TYR A1092 " (cutoff:3.500A) removed outlier: 10.290A pdb=" N GLY A1094 " --> pdb=" O GLY A 893 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE A1083 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE A1093 " --> pdb=" O LEU A1081 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A1081 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU A 900 " --> pdb=" O ARG A1080 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N LEU A1082 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA A 902 " --> pdb=" O LEU A1082 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N MET A1084 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N MET A 904 " --> pdb=" O MET A1084 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR A 901 " --> pdb=" O CYS A1065 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A1064 " --> pdb=" O VAL A1032 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A1066 " --> pdb=" O LEU A1034 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1417 through 1419 removed outlier: 3.604A pdb=" N PHE A1419 " --> pdb=" O CYS A1452 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1611 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: 8.46 Time building geometry restraints manager: 6.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10476 1.03 - 1.23: 52 1.23 - 1.42: 4726 1.42 - 1.62: 6064 1.62 - 1.81: 106 Bond restraints: 21424 Sorted by residual: bond pdb=" CB PRO A 97 " pdb=" CG PRO A 97 " ideal model delta sigma weight residual 1.492 1.609 -0.117 5.00e-02 4.00e+02 5.50e+00 bond pdb=" CA GLU A1036 " pdb=" C GLU A1036 " ideal model delta sigma weight residual 1.532 1.521 0.011 6.50e-03 2.37e+04 3.02e+00 bond pdb=" CB GLN A1085 " pdb=" CG GLN A1085 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.30e+00 bond pdb=" CB VAL A1091 " pdb=" CG2 VAL A1091 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.16e+00 bond pdb=" N PRO A 97 " pdb=" CA PRO A 97 " ideal model delta sigma weight residual 1.473 1.454 0.019 1.33e-02 5.65e+03 2.01e+00 ... (remaining 21419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.99: 38552 6.99 - 13.98: 2 13.98 - 20.97: 0 20.97 - 27.96: 0 27.96 - 34.95: 6 Bond angle restraints: 38560 Sorted by residual: angle pdb=" C ASP A 120 " pdb=" CA ASP A 120 " pdb=" HA ASP A 120 " ideal model delta sigma weight residual 109.00 74.05 34.95 3.00e+00 1.11e-01 1.36e+02 angle pdb=" N ARG A 517 " pdb=" CA ARG A 517 " pdb=" HA ARG A 517 " ideal model delta sigma weight residual 110.00 75.31 34.69 3.00e+00 1.11e-01 1.34e+02 angle pdb=" N ASP A 120 " pdb=" CA ASP A 120 " pdb=" HA ASP A 120 " ideal model delta sigma weight residual 110.00 75.49 34.51 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C ARG A 517 " pdb=" CA ARG A 517 " pdb=" HA ARG A 517 " ideal model delta sigma weight residual 109.00 74.78 34.22 3.00e+00 1.11e-01 1.30e+02 angle pdb=" CB ARG A 517 " pdb=" CA ARG A 517 " pdb=" HA ARG A 517 " ideal model delta sigma weight residual 109.00 75.46 33.54 3.00e+00 1.11e-01 1.25e+02 ... (remaining 38555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9275 17.92 - 35.84: 658 35.84 - 53.76: 184 53.76 - 71.68: 50 71.68 - 89.60: 14 Dihedral angle restraints: 10181 sinusoidal: 5344 harmonic: 4837 Sorted by residual: dihedral pdb=" CA TYR A1199 " pdb=" C TYR A1199 " pdb=" N TRP A1200 " pdb=" CA TRP A1200 " ideal model delta harmonic sigma weight residual 180.00 154.62 25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA LEU A 249 " pdb=" C LEU A 249 " pdb=" N PRO A 250 " pdb=" CA PRO A 250 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA ASN A 334 " pdb=" C ASN A 334 " pdb=" N ALA A 335 " pdb=" CA ALA A 335 " ideal model delta harmonic sigma weight residual -180.00 -159.64 -20.36 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 10178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1519 0.080 - 0.160: 95 0.160 - 0.240: 0 0.240 - 0.320: 0 0.320 - 0.399: 2 Chirality restraints: 1616 Sorted by residual: chirality pdb=" CA ARG A 517 " pdb=" N ARG A 517 " pdb=" C ARG A 517 " pdb=" CB ARG A 517 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA ASP A 120 " pdb=" N ASP A 120 " pdb=" C ASP A 120 " pdb=" CB ASP A 120 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CA PRO A 250 " pdb=" N PRO A 250 " pdb=" C PRO A 250 " pdb=" CB PRO A 250 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 1613 not shown) Planarity restraints: 3149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 96 " 0.100 5.00e-02 4.00e+02 1.40e-01 3.14e+01 pdb=" N PRO A 97 " -0.242 5.00e-02 4.00e+02 pdb=" CA PRO A 97 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 97 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1215 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" C PHE A1215 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE A1215 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN A1216 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A1290 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO A1291 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A1291 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1291 " 0.025 5.00e-02 4.00e+02 ... (remaining 3146 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 201 2.03 - 2.67: 31348 2.67 - 3.31: 61394 3.31 - 3.96: 76628 3.96 - 4.60: 122689 Nonbonded interactions: 292260 Sorted by model distance: nonbonded pdb=" OE1 GLN A1350 " pdb="HH12 ARG A1500 " model vdw 1.387 2.450 nonbonded pdb="HH22 ARG A 872 " pdb=" OD1 ASP A1159 " model vdw 1.553 2.450 nonbonded pdb=" H ASP A 120 " pdb=" HA ASP A 120 " model vdw 1.583 1.816 nonbonded pdb=" OD1 ASN A 303 " pdb=" H ASP A 304 " model vdw 1.588 2.450 nonbonded pdb=" OD1 ASP A1204 " pdb=" H TYR A1205 " model vdw 1.611 2.450 ... (remaining 292255 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.400 Extract box with map and model: 0.920 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 47.040 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 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 : 0.006 0.117 10926 Z= 0.389 Angle : 0.681 13.882 14809 Z= 0.407 Chirality : 0.043 0.399 1616 Planarity : 0.005 0.140 1872 Dihedral : 13.857 89.596 3919 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.23), residues: 1321 helix: 0.40 (0.19), residues: 737 sheet: -1.77 (0.61), residues: 67 loop : -1.49 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1200 HIS 0.003 0.001 HIS A 870 PHE 0.014 0.002 PHE A1276 TYR 0.016 0.002 TYR A1434 ARG 0.007 0.001 ARG A 517 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 306 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 TYR cc_start: 0.8014 (m-80) cc_final: 0.7744 (m-80) REVERT: A 497 TYR cc_start: 0.7405 (m-80) cc_final: 0.6860 (m-80) REVERT: A 1075 MET cc_start: 0.6595 (mmm) cc_final: 0.5719 (tmm) REVERT: A 1287 PHE cc_start: 0.7008 (m-80) cc_final: 0.6753 (t80) REVERT: A 1386 MET cc_start: 0.8197 (tpt) cc_final: 0.7947 (tpt) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.5001 time to fit residues: 216.4025 Evaluate side-chains 176 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN A 470 ASN A 530 ASN A 619 ASN ** A1262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10926 Z= 0.286 Angle : 0.634 7.143 14809 Z= 0.344 Chirality : 0.044 0.380 1616 Planarity : 0.005 0.066 1872 Dihedral : 4.931 22.655 1460 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.75 % Allowed : 8.73 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.23), residues: 1321 helix: 0.52 (0.19), residues: 752 sheet: -1.50 (0.61), residues: 66 loop : -1.21 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 131 HIS 0.007 0.001 HIS A 768 PHE 0.020 0.002 PHE A1248 TYR 0.018 0.002 TYR A 680 ARG 0.007 0.001 ARG A1500 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 192 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 ASP cc_start: 0.7741 (m-30) cc_final: 0.7491 (m-30) REVERT: A 554 TYR cc_start: 0.8319 (t80) cc_final: 0.8074 (t80) REVERT: A 562 PHE cc_start: 0.8041 (m-10) cc_final: 0.7811 (m-10) REVERT: A 672 MET cc_start: 0.6855 (mtp) cc_final: 0.6650 (mtp) REVERT: A 868 ILE cc_start: 0.7520 (mt) cc_final: 0.7189 (mp) REVERT: A 1031 LEU cc_start: 0.7992 (mp) cc_final: 0.7776 (mt) REVERT: A 1103 MET cc_start: 0.8147 (tmm) cc_final: 0.7907 (ppp) REVERT: A 1267 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7846 (mt-10) REVERT: A 1497 TRP cc_start: 0.8029 (t60) cc_final: 0.7282 (t60) outliers start: 20 outliers final: 13 residues processed: 205 average time/residue: 0.4441 time to fit residues: 136.2198 Evaluate side-chains 184 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 171 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 787 PHE Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1302 PHE Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain A residue 1485 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 ASN A1061 GLN A1085 GLN A1261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10926 Z= 0.316 Angle : 0.606 7.314 14809 Z= 0.326 Chirality : 0.042 0.382 1616 Planarity : 0.005 0.050 1872 Dihedral : 4.788 24.107 1460 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.92 % Allowed : 11.27 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.23), residues: 1321 helix: 0.74 (0.19), residues: 755 sheet: -1.60 (0.58), residues: 67 loop : -1.33 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1200 HIS 0.005 0.001 HIS A1136 PHE 0.040 0.002 PHE A 759 TYR 0.013 0.002 TYR A 594 ARG 0.009 0.001 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 MET cc_start: 0.7671 (mpp) cc_final: 0.7428 (mpp) REVERT: A 868 ILE cc_start: 0.8399 (mt) cc_final: 0.8150 (tt) REVERT: A 1031 LEU cc_start: 0.8579 (mp) cc_final: 0.8378 (mt) REVERT: A 1243 MET cc_start: 0.8588 (mtp) cc_final: 0.8382 (mtp) REVERT: A 1361 LEU cc_start: 0.7729 (tt) cc_final: 0.7452 (mt) outliers start: 22 outliers final: 14 residues processed: 178 average time/residue: 0.4420 time to fit residues: 117.7573 Evaluate side-chains 163 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1061 GLN Chi-restraints excluded: chain A residue 1277 SER Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1485 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10926 Z= 0.295 Angle : 0.553 7.361 14809 Z= 0.296 Chirality : 0.041 0.383 1616 Planarity : 0.004 0.057 1872 Dihedral : 4.659 22.535 1460 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.75 % Allowed : 13.62 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.23), residues: 1321 helix: 0.89 (0.19), residues: 758 sheet: -1.48 (0.57), residues: 67 loop : -1.31 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 131 HIS 0.004 0.001 HIS A 870 PHE 0.018 0.001 PHE A 759 TYR 0.013 0.001 TYR A 594 ARG 0.008 0.000 ARG A1163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 158 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 PHE cc_start: 0.8365 (m-80) cc_final: 0.8015 (m-10) REVERT: A 868 ILE cc_start: 0.8440 (mt) cc_final: 0.8187 (tt) REVERT: A 1103 MET cc_start: 0.8168 (tmm) cc_final: 0.7963 (tmm) REVERT: A 1123 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7116 (tm-30) REVERT: A 1361 LEU cc_start: 0.7802 (tt) cc_final: 0.7398 (mt) outliers start: 20 outliers final: 16 residues processed: 168 average time/residue: 0.4387 time to fit residues: 113.7704 Evaluate side-chains 164 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1302 PHE Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1485 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1061 GLN A1456 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.5909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10926 Z= 0.246 Angle : 0.530 7.340 14809 Z= 0.281 Chirality : 0.040 0.383 1616 Planarity : 0.004 0.055 1872 Dihedral : 4.457 21.721 1460 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.83 % Allowed : 14.15 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.23), residues: 1321 helix: 0.99 (0.19), residues: 765 sheet: -1.42 (0.56), residues: 73 loop : -1.42 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1200 HIS 0.004 0.001 HIS A1059 PHE 0.012 0.001 PHE A1454 TYR 0.013 0.001 TYR A 594 ARG 0.007 0.000 ARG A1163 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 SER cc_start: 0.7897 (OUTLIER) cc_final: 0.7559 (t) REVERT: A 390 TYR cc_start: 0.8600 (t80) cc_final: 0.8151 (t80) REVERT: A 664 SER cc_start: 0.8852 (p) cc_final: 0.8436 (m) REVERT: A 868 ILE cc_start: 0.8512 (mt) cc_final: 0.8255 (tt) REVERT: A 1123 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7291 (tm-30) REVERT: A 1243 MET cc_start: 0.8665 (mtp) cc_final: 0.8461 (mtp) REVERT: A 1361 LEU cc_start: 0.7904 (tt) cc_final: 0.7227 (mt) REVERT: A 1414 TYR cc_start: 0.7710 (p90) cc_final: 0.7411 (p90) outliers start: 21 outliers final: 15 residues processed: 174 average time/residue: 0.4199 time to fit residues: 112.4673 Evaluate side-chains 165 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1061 GLN Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1365 MET Chi-restraints excluded: chain A residue 1485 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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: 0.7746 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10926 Z= 0.202 Angle : 0.506 7.186 14809 Z= 0.267 Chirality : 0.039 0.378 1616 Planarity : 0.004 0.042 1872 Dihedral : 4.381 21.900 1460 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.75 % Allowed : 15.02 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.24), residues: 1321 helix: 1.11 (0.19), residues: 767 sheet: -1.25 (0.58), residues: 73 loop : -1.39 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1200 HIS 0.003 0.001 HIS A 870 PHE 0.012 0.001 PHE A 759 TYR 0.009 0.001 TYR A 680 ARG 0.003 0.000 ARG A1163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 TYR cc_start: 0.8560 (t80) cc_final: 0.8197 (t80) REVERT: A 562 PHE cc_start: 0.8395 (m-80) cc_final: 0.7981 (m-10) REVERT: A 664 SER cc_start: 0.8843 (p) cc_final: 0.8427 (m) REVERT: A 868 ILE cc_start: 0.8526 (mt) cc_final: 0.8288 (tt) REVERT: A 1123 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7343 (tm-30) REVERT: A 1361 LEU cc_start: 0.7809 (tt) cc_final: 0.7260 (mt) REVERT: A 1414 TYR cc_start: 0.7842 (p90) cc_final: 0.7564 (p90) outliers start: 20 outliers final: 16 residues processed: 171 average time/residue: 0.3897 time to fit residues: 102.6765 Evaluate side-chains 163 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 963 GLU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1277 SER Chi-restraints excluded: chain A residue 1302 PHE Chi-restraints excluded: chain A residue 1485 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1061 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.6313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10926 Z= 0.178 Angle : 0.493 7.316 14809 Z= 0.259 Chirality : 0.038 0.377 1616 Planarity : 0.004 0.040 1872 Dihedral : 4.212 21.608 1460 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.48 % Allowed : 15.81 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.24), residues: 1321 helix: 1.27 (0.19), residues: 768 sheet: -1.01 (0.59), residues: 73 loop : -1.34 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1200 HIS 0.003 0.001 HIS A 870 PHE 0.011 0.001 PHE A 759 TYR 0.009 0.001 TYR A 680 ARG 0.005 0.000 ARG A1163 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 TYR cc_start: 0.8591 (t80) cc_final: 0.8209 (t80) REVERT: A 562 PHE cc_start: 0.8398 (m-80) cc_final: 0.7942 (m-10) REVERT: A 664 SER cc_start: 0.8854 (p) cc_final: 0.8438 (m) REVERT: A 779 MET cc_start: 0.7528 (tpp) cc_final: 0.7315 (tpp) REVERT: A 868 ILE cc_start: 0.8513 (mt) cc_final: 0.8284 (tt) REVERT: A 1123 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7330 (tm-30) REVERT: A 1361 LEU cc_start: 0.7791 (tt) cc_final: 0.7258 (mt) REVERT: A 1414 TYR cc_start: 0.7898 (p90) cc_final: 0.7613 (p90) outliers start: 17 outliers final: 15 residues processed: 163 average time/residue: 0.4270 time to fit residues: 106.7408 Evaluate side-chains 163 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 963 GLU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1277 SER Chi-restraints excluded: chain A residue 1302 PHE Chi-restraints excluded: chain A residue 1485 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.7729 moved from start: 0.6473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10926 Z= 0.147 Angle : 0.477 7.149 14809 Z= 0.249 Chirality : 0.038 0.375 1616 Planarity : 0.003 0.039 1872 Dihedral : 4.081 21.302 1460 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.96 % Allowed : 16.59 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.24), residues: 1321 helix: 1.43 (0.20), residues: 767 sheet: -1.11 (0.56), residues: 86 loop : -1.23 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1200 HIS 0.002 0.000 HIS A 870 PHE 0.011 0.001 PHE A 759 TYR 0.009 0.001 TYR A 680 ARG 0.002 0.000 ARG A1163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 154 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7720 (p0) REVERT: A 390 TYR cc_start: 0.8574 (t80) cc_final: 0.8194 (t80) REVERT: A 562 PHE cc_start: 0.8410 (m-80) cc_final: 0.7967 (m-10) REVERT: A 664 SER cc_start: 0.8844 (p) cc_final: 0.8438 (m) REVERT: A 868 ILE cc_start: 0.8572 (mt) cc_final: 0.8335 (tt) REVERT: A 1123 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7227 (tm-30) REVERT: A 1328 TRP cc_start: 0.8438 (t60) cc_final: 0.7872 (t60) REVERT: A 1361 LEU cc_start: 0.7788 (tt) cc_final: 0.7230 (mt) REVERT: A 1386 MET cc_start: 0.8049 (tpt) cc_final: 0.7669 (tpt) REVERT: A 1414 TYR cc_start: 0.7852 (p90) cc_final: 0.7564 (p90) outliers start: 11 outliers final: 10 residues processed: 162 average time/residue: 0.4087 time to fit residues: 101.0774 Evaluate side-chains 159 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 963 GLU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1277 SER Chi-restraints excluded: chain A residue 1485 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 119 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 78 optimal weight: 0.0970 chunk 126 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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: 0.7710 moved from start: 0.6549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10926 Z= 0.135 Angle : 0.474 8.051 14809 Z= 0.245 Chirality : 0.038 0.373 1616 Planarity : 0.003 0.040 1872 Dihedral : 3.951 20.790 1460 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.05 % Allowed : 16.77 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.24), residues: 1321 helix: 1.59 (0.20), residues: 767 sheet: -1.01 (0.56), residues: 86 loop : -1.10 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1200 HIS 0.002 0.000 HIS A 870 PHE 0.009 0.001 PHE A 759 TYR 0.008 0.001 TYR A1414 ARG 0.002 0.000 ARG A1163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7760 (p0) REVERT: A 390 TYR cc_start: 0.8602 (t80) cc_final: 0.8245 (t80) REVERT: A 562 PHE cc_start: 0.8406 (m-80) cc_final: 0.7988 (m-10) REVERT: A 664 SER cc_start: 0.8817 (p) cc_final: 0.8381 (m) REVERT: A 779 MET cc_start: 0.7433 (tpp) cc_final: 0.7130 (mmm) REVERT: A 868 ILE cc_start: 0.8581 (mt) cc_final: 0.8310 (tt) REVERT: A 1123 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7165 (tm-30) REVERT: A 1328 TRP cc_start: 0.8451 (t60) cc_final: 0.7903 (t60) REVERT: A 1361 LEU cc_start: 0.7764 (tt) cc_final: 0.7229 (mt) REVERT: A 1386 MET cc_start: 0.8012 (tpt) cc_final: 0.7630 (tpt) REVERT: A 1414 TYR cc_start: 0.7788 (p90) cc_final: 0.7481 (p90) outliers start: 12 outliers final: 10 residues processed: 167 average time/residue: 0.4078 time to fit residues: 104.0481 Evaluate side-chains 162 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 963 GLU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1277 SER Chi-restraints excluded: chain A residue 1302 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 87 optimal weight: 0.3980 chunk 132 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.7718 moved from start: 0.6697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10926 Z= 0.147 Angle : 0.476 7.285 14809 Z= 0.247 Chirality : 0.038 0.375 1616 Planarity : 0.003 0.039 1872 Dihedral : 3.897 20.240 1460 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.96 % Allowed : 17.12 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.24), residues: 1321 helix: 1.68 (0.20), residues: 765 sheet: -1.00 (0.57), residues: 86 loop : -1.09 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1200 HIS 0.002 0.000 HIS A 870 PHE 0.019 0.001 PHE A1078 TYR 0.008 0.001 TYR A 680 ARG 0.002 0.000 ARG A1163 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 154 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7788 (p0) REVERT: A 390 TYR cc_start: 0.8621 (t80) cc_final: 0.8267 (t80) REVERT: A 562 PHE cc_start: 0.8378 (m-80) cc_final: 0.7958 (m-10) REVERT: A 664 SER cc_start: 0.8827 (p) cc_final: 0.8391 (m) REVERT: A 868 ILE cc_start: 0.8579 (mt) cc_final: 0.8308 (tt) REVERT: A 951 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8276 (tm-30) REVERT: A 1123 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7141 (tm-30) REVERT: A 1328 TRP cc_start: 0.8465 (t60) cc_final: 0.7900 (t60) REVERT: A 1361 LEU cc_start: 0.7773 (tt) cc_final: 0.7228 (mt) outliers start: 11 outliers final: 10 residues processed: 162 average time/residue: 0.4197 time to fit residues: 103.8530 Evaluate side-chains 163 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 152 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 963 GLU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1277 SER Chi-restraints excluded: chain A residue 1302 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.0470 chunk 97 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.128012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110844 restraints weight = 45703.316| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.35 r_work: 0.3153 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.6774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10926 Z= 0.152 Angle : 0.474 7.345 14809 Z= 0.246 Chirality : 0.038 0.375 1616 Planarity : 0.003 0.039 1872 Dihedral : 3.874 20.175 1460 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.87 % Allowed : 17.38 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.24), residues: 1321 helix: 1.70 (0.19), residues: 765 sheet: -0.95 (0.57), residues: 86 loop : -1.08 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 514 HIS 0.002 0.000 HIS A 870 PHE 0.011 0.001 PHE A1078 TYR 0.008 0.001 TYR A 680 ARG 0.002 0.000 ARG A1163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4673.62 seconds wall clock time: 85 minutes 41.76 seconds (5141.76 seconds total)