Starting phenix.real_space_refine on Fri Mar 6 01:51:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mvz_24059/03_2026/7mvz_24059.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mvz_24059/03_2026/7mvz_24059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mvz_24059/03_2026/7mvz_24059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mvz_24059/03_2026/7mvz_24059.map" model { file = "/net/cci-nas-00/data/ceres_data/7mvz_24059/03_2026/7mvz_24059.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mvz_24059/03_2026/7mvz_24059.cif" } resolution = 2.81 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= -0.002 sd= 0.053 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 56 5.16 5 C 8522 2.51 5 N 2291 2.21 5 O 2443 1.98 5 H 13421 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26733 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 25701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1641, 25701 Classifications: {'peptide': 1641} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1570} Chain breaks: 14 Chain: "B" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 854 Classifications: {'peptide': 53} Link IDs: {'TRANS': 52} Chain: "C" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 178 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Time building chain proxies: 4.36, per 1000 atoms: 0.16 Number of scatterers: 26733 At special positions: 0 Unit cell: (80.352, 110.16, 186.624, 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 56 16.00 O 2443 8.00 N 2291 7.00 C 8522 6.00 H 13421 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 681.2 milliseconds 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 1 sheets defined 76.4% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 43 through 52 Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 61 through 67 removed outlier: 3.710A pdb=" N VAL A 65 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 80 Processing helix chain 'A' and resid 89 through 103 Processing helix chain 'A' and resid 106 through 120 Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 173 through 205 Processing helix chain 'A' and resid 211 through 226 Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 242 through 249 removed outlier: 4.089A pdb=" N THR A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 3.911A pdb=" N ASP A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 299 Processing helix chain 'A' and resid 306 through 321 removed outlier: 3.816A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 332 through 352 Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 352 through 363 Processing helix chain 'A' and resid 371 through 374 Processing helix chain 'A' and resid 375 through 393 removed outlier: 3.554A pdb=" N GLY A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 418 removed outlier: 4.806A pdb=" N VAL A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 413 " --> pdb=" O HIS A 409 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 removed outlier: 3.839A pdb=" N PHE A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN A 471 " --> pdb=" O PHE A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 489 Processing helix chain 'A' and resid 491 through 504 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.176A pdb=" N LEU A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL A 523 " --> pdb=" O ARG A 519 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 551 Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.630A pdb=" N ASP A 557 " --> pdb=" O GLN A 554 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 558 " --> pdb=" O TYR A 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 554 through 558' Processing helix chain 'A' and resid 564 through 577 removed outlier: 3.565A pdb=" N ASN A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TYR A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N MET A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU A 575 " --> pdb=" O TYR A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 removed outlier: 3.541A pdb=" N GLN A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 591 Processing helix chain 'A' and resid 595 through 610 removed outlier: 4.207A pdb=" N PHE A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 617 removed outlier: 3.852A pdb=" N ALA A 617 " --> pdb=" O LYS A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 626 Processing helix chain 'A' and resid 635 through 641 removed outlier: 4.199A pdb=" N ARG A 640 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 719 Processing helix chain 'A' and resid 731 through 755 removed outlier: 3.599A pdb=" N THR A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 771 Processing helix chain 'A' and resid 779 through 792 Processing helix chain 'A' and resid 800 through 819 removed outlier: 4.164A pdb=" N ALA A 819 " --> pdb=" O HIS A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 830 Processing helix chain 'A' and resid 843 through 848 removed outlier: 3.654A pdb=" N ARG A 846 " --> pdb=" O ARG A 843 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 847 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 848 " --> pdb=" O SER A 845 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 843 through 848' Processing helix chain 'A' and resid 854 through 877 removed outlier: 4.581A pdb=" N LEU A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A 861 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 863 " --> pdb=" O ASP A 859 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS A 877 " --> pdb=" O ASP A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 926 Processing helix chain 'A' and resid 933 through 957 removed outlier: 4.221A pdb=" N ARG A 937 " --> pdb=" O SER A 933 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 964 removed outlier: 3.648A pdb=" N THR A 963 " --> pdb=" O SER A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 979 removed outlier: 3.521A pdb=" N THR A 979 " --> pdb=" O SER A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1001 Processing helix chain 'A' and resid 1008 through 1035 Processing helix chain 'A' and resid 1042 through 1055 removed outlier: 4.291A pdb=" N HIS A1046 " --> pdb=" O PRO A1042 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A1049 " --> pdb=" O THR A1045 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A1053 " --> pdb=" O GLN A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1060 Processing helix chain 'A' and resid 1061 through 1063 No H-bonds generated for 'chain 'A' and resid 1061 through 1063' Processing helix chain 'A' and resid 1064 through 1081 Processing helix chain 'A' and resid 1091 through 1097 removed outlier: 3.859A pdb=" N TYR A1095 " --> pdb=" O SER A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1109 Processing helix chain 'A' and resid 1118 through 1134 Processing helix chain 'A' and resid 1137 through 1146 Processing helix chain 'A' and resid 1169 through 1179 removed outlier: 3.723A pdb=" N ALA A1173 " --> pdb=" O SER A1169 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU A1176 " --> pdb=" O ALA A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1203 removed outlier: 3.817A pdb=" N ALA A1191 " --> pdb=" O GLN A1187 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A1202 " --> pdb=" O SER A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1214 removed outlier: 3.512A pdb=" N ILE A1207 " --> pdb=" O TRP A1203 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A1209 " --> pdb=" O TRP A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1228 removed outlier: 3.751A pdb=" N ASP A1218 " --> pdb=" O LYS A1214 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU A1220 " --> pdb=" O VAL A1216 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG A1221 " --> pdb=" O VAL A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1267 removed outlier: 3.911A pdb=" N PHE A1244 " --> pdb=" O ALA A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1277 Processing helix chain 'A' and resid 1280 through 1287 Processing helix chain 'A' and resid 1294 through 1309 removed outlier: 3.682A pdb=" N HIS A1298 " --> pdb=" O ASN A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1318 removed outlier: 3.570A pdb=" N PHE A1317 " --> pdb=" O VAL A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1342 removed outlier: 4.384A pdb=" N GLN A1340 " --> pdb=" O GLU A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1354 removed outlier: 4.002A pdb=" N GLN A1353 " --> pdb=" O GLY A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1391 removed outlier: 4.020A pdb=" N GLU A1359 " --> pdb=" O GLY A1355 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A1389 " --> pdb=" O LEU A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1417 removed outlier: 3.559A pdb=" N GLN A1416 " --> pdb=" O LEU A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1447 removed outlier: 3.974A pdb=" N ALA A1436 " --> pdb=" O ARG A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1466 removed outlier: 3.756A pdb=" N LEU A1456 " --> pdb=" O ASP A1452 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ALA A1458 " --> pdb=" O THR A1454 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU A1459 " --> pdb=" O HIS A1455 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL A1460 " --> pdb=" O LEU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1496 removed outlier: 3.741A pdb=" N GLY A1496 " --> pdb=" O ALA A1492 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1518 removed outlier: 4.477A pdb=" N THR A1513 " --> pdb=" O GLN A1509 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE A1514 " --> pdb=" O GLN A1510 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A1515 " --> pdb=" O VAL A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1531 removed outlier: 3.564A pdb=" N HIS A1531 " --> pdb=" O ALA A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1544 through 1559 Processing helix chain 'A' and resid 1561 through 1565 Processing helix chain 'A' and resid 1567 through 1578 removed outlier: 4.106A pdb=" N ASN A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE A1574 " --> pdb=" O GLN A1570 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N HIS A1578 " --> pdb=" O ILE A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1589 removed outlier: 3.905A pdb=" N VAL A1583 " --> pdb=" O ASP A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1619 through 1632 Processing helix chain 'A' and resid 1634 through 1643 Processing helix chain 'A' and resid 1643 through 1653 removed outlier: 4.211A pdb=" N LEU A1647 " --> pdb=" O CYS A1643 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS A1649 " --> pdb=" O GLY A1645 " (cutoff:3.500A) Processing helix chain 'A' and resid 1655 through 1661 removed outlier: 3.639A pdb=" N ARG A1661 " --> pdb=" O GLY A1657 " (cutoff:3.500A) Processing helix chain 'A' and resid 1670 through 1683 removed outlier: 3.543A pdb=" N CYS A1683 " --> pdb=" O ILE A1679 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1695 removed outlier: 3.595A pdb=" N ALA A1694 " --> pdb=" O ASN A1690 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A1695 " --> pdb=" O ILE A1691 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1710 Processing helix chain 'A' and resid 1710 through 1721 removed outlier: 4.370A pdb=" N LEU A1714 " --> pdb=" O PHE A1710 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE A1721 " --> pdb=" O SER A1717 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1766 removed outlier: 3.520A pdb=" N GLU A1750 " --> pdb=" O LEU A1746 " (cutoff:3.500A) Processing helix chain 'A' and resid 1779 through 1789 Processing helix chain 'A' and resid 1794 through 1800 removed outlier: 3.967A pdb=" N ARG A1799 " --> pdb=" O LEU A1796 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A1800 " --> pdb=" O ARG A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1834 through 1849 Processing helix chain 'B' and resid 248 through 254 Processing helix chain 'B' and resid 259 through 299 removed outlier: 4.001A pdb=" N MET B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY B 267 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU B 268 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA B 277 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 630 through 632 removed outlier: 3.757A pdb=" N VAL A 632 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 688 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 654 " --> pdb=" O GLY A 688 " (cutoff:3.500A) 840 hydrogen bonds defined for protein. 2469 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: 6.66 Time building geometry restraints manager: 3.19 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: 13397 1.03 - 1.23: 26 1.23 - 1.42: 5593 1.42 - 1.62: 7889 1.62 - 1.81: 88 Bond restraints: 26993 Sorted by residual: bond pdb=" N ARG A 530 " pdb=" H ARG A 530 " ideal model delta sigma weight residual 0.860 0.910 -0.050 2.00e-02 2.50e+03 6.36e+00 bond pdb=" N ALA A 532 " pdb=" H ALA A 532 " ideal model delta sigma weight residual 0.860 0.910 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" N SER A 531 " pdb=" CA SER A 531 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.32e-02 5.74e+03 5.92e+00 bond pdb=" N SER A 531 " pdb=" H SER A 531 " ideal model delta sigma weight residual 0.860 0.903 -0.043 2.00e-02 2.50e+03 4.72e+00 bond pdb=" N ARG A 530 " pdb=" CA ARG A 530 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.33e-02 5.65e+03 4.15e+00 ... (remaining 26988 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 48210 1.53 - 3.06: 553 3.06 - 4.59: 82 4.59 - 6.12: 6 6.12 - 7.65: 3 Bond angle restraints: 48854 Sorted by residual: angle pdb=" CA LYS A 529 " pdb=" C LYS A 529 " pdb=" N ARG A 530 " ideal model delta sigma weight residual 117.30 113.32 3.98 1.16e+00 7.43e-01 1.18e+01 angle pdb=" O LYS A 529 " pdb=" C LYS A 529 " pdb=" N ARG A 530 " ideal model delta sigma weight residual 122.12 125.09 -2.97 1.06e+00 8.90e-01 7.83e+00 angle pdb=" N VAL A1165 " pdb=" CA VAL A1165 " pdb=" C VAL A1165 " ideal model delta sigma weight residual 111.00 103.35 7.65 2.80e+00 1.28e-01 7.46e+00 angle pdb=" C LYS A 529 " pdb=" N ARG A 530 " pdb=" CA ARG A 530 " ideal model delta sigma weight residual 121.14 125.77 -4.63 1.75e+00 3.27e-01 7.01e+00 angle pdb=" N ALA A 532 " pdb=" CA ALA A 532 " pdb=" C ALA A 532 " ideal model delta sigma weight residual 111.03 108.19 2.84 1.11e+00 8.12e-01 6.56e+00 ... (remaining 48849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 12120 17.78 - 35.56: 305 35.56 - 53.34: 157 53.34 - 71.12: 53 71.12 - 88.90: 2 Dihedral angle restraints: 12637 sinusoidal: 6839 harmonic: 5798 Sorted by residual: dihedral pdb=" CA CYS A 821 " pdb=" CB CYS A 821 " pdb=" SG CYS A 821 " pdb=" HG CYS A 821 " ideal model delta sinusoidal sigma weight residual 60.00 0.60 59.40 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ASP A 759 " pdb=" CB ASP A 759 " pdb=" CG ASP A 759 " pdb=" OD1 ASP A 759 " ideal model delta sinusoidal sigma weight residual -30.00 -79.74 49.74 1 2.00e+01 2.50e-03 8.49e+00 dihedral pdb=" N LEU A 774 " pdb=" CA LEU A 774 " pdb=" CB LEU A 774 " pdb=" CG LEU A 774 " ideal model delta sinusoidal sigma weight residual -60.00 -104.84 44.84 3 1.50e+01 4.44e-03 8.07e+00 ... (remaining 12634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1655 0.033 - 0.066: 379 0.066 - 0.099: 110 0.099 - 0.132: 20 0.132 - 0.165: 3 Chirality restraints: 2167 Sorted by residual: chirality pdb=" CA ILE A 535 " pdb=" N ILE A 535 " pdb=" C ILE A 535 " pdb=" CB ILE A 535 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA VAL A1165 " pdb=" N VAL A1165 " pdb=" C VAL A1165 " pdb=" CB VAL A1165 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CA ILE A 682 " pdb=" N ILE A 682 " pdb=" C ILE A 682 " pdb=" CB ILE A 682 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 2164 not shown) Planarity restraints: 3975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 530 " -0.129 9.50e-02 1.11e+02 6.40e-02 5.21e+01 pdb=" NE ARG A 530 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 530 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 530 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 530 " -0.009 2.00e-02 2.50e+03 pdb="HH11 ARG A 530 " -0.017 2.00e-02 2.50e+03 pdb="HH12 ARG A 530 " 0.057 2.00e-02 2.50e+03 pdb="HH21 ARG A 530 " 0.084 2.00e-02 2.50e+03 pdb="HH22 ARG A 530 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1670 " -0.022 2.00e-02 2.50e+03 3.67e-02 2.02e+01 pdb=" CG ASN A1670 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A1670 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A1670 " -0.063 2.00e-02 2.50e+03 pdb="HD21 ASN A1670 " -0.001 2.00e-02 2.50e+03 pdb="HD22 ASN A1670 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1397 " -0.018 2.00e-02 2.50e+03 3.12e-02 1.46e+01 pdb=" CG ASN A1397 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A1397 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A1397 " -0.054 2.00e-02 2.50e+03 pdb="HD21 ASN A1397 " -0.001 2.00e-02 2.50e+03 pdb="HD22 ASN A1397 " 0.034 2.00e-02 2.50e+03 ... (remaining 3972 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 2002 2.23 - 2.82: 59597 2.82 - 3.41: 71758 3.41 - 4.01: 91023 4.01 - 4.60: 145388 Nonbonded interactions: 369768 Sorted by model distance: nonbonded pdb=" O MET A1659 " pdb="HD21 ASN A1712 " model vdw 1.633 2.450 nonbonded pdb=" OE1 GLU A 905 " pdb=" H GLU A 905 " model vdw 1.636 2.450 nonbonded pdb=" HE1 TRP A 638 " pdb=" O SER A 725 " model vdw 1.641 2.450 nonbonded pdb=" O PHE A 581 " pdb=" HG1 THR A 585 " model vdw 1.646 2.450 nonbonded pdb=" OE1 GLU A1336 " pdb=" H GLU A1336 " model vdw 1.647 2.450 ... (remaining 369763 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=0.81 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.280 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 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 : 0.002 0.034 13572 Z= 0.105 Angle : 0.478 7.646 18446 Z= 0.254 Chirality : 0.032 0.165 2167 Planarity : 0.004 0.048 2354 Dihedral : 7.604 85.418 4902 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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 (0.20), residues: 1673 helix: -0.10 (0.15), residues: 1132 sheet: -2.50 (1.41), residues: 9 loop : -1.93 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1325 TYR 0.018 0.001 TYR A 533 PHE 0.015 0.001 PHE B 278 TRP 0.005 0.001 TRP A1205 HIS 0.001 0.000 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00202 (13572) covalent geometry : angle 0.47799 (18446) hydrogen bonds : bond 0.12453 ( 840) hydrogen bonds : angle 5.17551 ( 2469) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 397 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 0.687 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: 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: 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: 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 578 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8059 (pp20) REVERT: A 586 MET cc_start: 0.7666 (mmm) cc_final: 0.7423 (mmm) REVERT: A 1193 MET cc_start: 0.8132 (mmm) cc_final: 0.7887 (mmm) REVERT: A 1400 PHE cc_start: 0.5174 (t80) cc_final: 0.4881 (t80) REVERT: A 1566 GLN cc_start: 0.9030 (mm110) cc_final: 0.8826 (mm-40) REVERT: B 280 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7861 (pp20) outliers start: 0 outliers final: 1 residues processed: 397 average time/residue: 1.0939 time to fit residues: 479.2520 Evaluate side-chains 198 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.0770 chunk 91 optimal weight: 0.0570 chunk 149 optimal weight: 2.9990 overall best weight: 1.1460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN A 652 ASN ** A1510 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 = 0.4481 r_free = 0.4481 target = 0.126100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.109374 restraints weight = 127616.554| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 4.32 r_work: 0.4099 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4110 r_free = 0.4110 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4109 r_free = 0.4109 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13572 Z= 0.153 Angle : 0.554 5.733 18446 Z= 0.285 Chirality : 0.034 0.151 2167 Planarity : 0.005 0.081 2354 Dihedral : 3.040 42.457 1841 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.56 % Allowed : 13.85 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.20 (0.21), residues: 1673 helix: 0.85 (0.15), residues: 1154 sheet: -2.71 (1.24), residues: 9 loop : -1.40 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1013 TYR 0.012 0.001 TYR A1008 PHE 0.019 0.002 PHE A1581 TRP 0.017 0.001 TRP A1138 HIS 0.006 0.001 HIS A1465 Details of bonding type rmsd covalent geometry : bond 0.00336 (13572) covalent geometry : angle 0.55404 (18446) hydrogen bonds : bond 0.03702 ( 840) hydrogen bonds : angle 4.13525 ( 2469) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.532 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: 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: 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 167 MET cc_start: 0.7863 (tpp) cc_final: 0.7613 (ttp) REVERT: A 211 HIS cc_start: 0.7636 (t-170) cc_final: 0.7296 (t-90) REVERT: A 350 MET cc_start: 0.8718 (mtp) cc_final: 0.8455 (mtp) REVERT: A 387 THR cc_start: 0.8018 (m) cc_final: 0.7810 (p) REVERT: A 490 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.8077 (tpm170) REVERT: A 578 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8197 (pp20) REVERT: A 1320 THR cc_start: 0.7287 (OUTLIER) cc_final: 0.7021 (m) REVERT: B 276 ASP cc_start: 0.7469 (m-30) cc_final: 0.6842 (p0) REVERT: B 280 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8094 (pp20) outliers start: 36 outliers final: 18 residues processed: 222 average time/residue: 1.0763 time to fit residues: 264.2469 Evaluate side-chains 180 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1265 GLN Chi-restraints excluded: chain A residue 1320 THR Chi-restraints excluded: chain A residue 1475 ASP Chi-restraints excluded: chain A residue 1572 LEU Chi-restraints excluded: chain A residue 1847 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 116 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 0.0980 chunk 121 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN A 652 ASN A1510 GLN B 282 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.122223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.105078 restraints weight = 127793.729| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 4.28 r_work: 0.4023 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4036 r_free = 0.4036 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4036 r_free = 0.4036 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13572 Z= 0.156 Angle : 0.533 5.553 18446 Z= 0.273 Chirality : 0.034 0.144 2167 Planarity : 0.004 0.083 2354 Dihedral : 2.928 11.878 1838 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.41 % Allowed : 16.05 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.76 (0.21), residues: 1673 helix: 1.31 (0.15), residues: 1156 sheet: -2.63 (1.28), residues: 9 loop : -1.30 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1267 TYR 0.011 0.001 TYR A1282 PHE 0.017 0.002 PHE A 581 TRP 0.009 0.001 TRP A1322 HIS 0.004 0.001 HIS A 815 Details of bonding type rmsd covalent geometry : bond 0.00337 (13572) covalent geometry : angle 0.53346 (18446) hydrogen bonds : bond 0.03369 ( 840) hydrogen bonds : angle 3.95811 ( 2469) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 0.490 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: 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: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.8028 (tpp) cc_final: 0.7704 (ttp) REVERT: A 211 HIS cc_start: 0.7681 (t-170) cc_final: 0.7457 (t-90) REVERT: A 350 MET cc_start: 0.8721 (mtp) cc_final: 0.8479 (mtp) REVERT: A 490 ARG cc_start: 0.8354 (mtm-85) cc_final: 0.8068 (tpm170) REVERT: A 578 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8382 (pp20) REVERT: A 633 ASP cc_start: 0.7236 (t0) cc_final: 0.6971 (t0) REVERT: A 1193 MET cc_start: 0.8029 (mmm) cc_final: 0.7821 (mmm) REVERT: A 1320 THR cc_start: 0.7637 (OUTLIER) cc_final: 0.7388 (m) REVERT: B 276 ASP cc_start: 0.7620 (m-30) cc_final: 0.6821 (p0) REVERT: B 280 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8212 (pp20) outliers start: 34 outliers final: 17 residues processed: 192 average time/residue: 1.0204 time to fit residues: 217.9406 Evaluate side-chains 165 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1183 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1320 THR Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1400 PHE Chi-restraints excluded: chain A residue 1413 GLU Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain A residue 1475 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 9 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN A 652 ASN B 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.114917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.097400 restraints weight = 125830.772| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 4.19 r_work: 0.3866 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13572 Z= 0.210 Angle : 0.601 6.657 18446 Z= 0.312 Chirality : 0.036 0.220 2167 Planarity : 0.005 0.054 2354 Dihedral : 3.406 15.831 1838 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.55 % Allowed : 14.91 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.80 (0.21), residues: 1673 helix: 1.34 (0.15), residues: 1155 sheet: -2.59 (1.50), residues: 9 loop : -1.29 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1013 TYR 0.022 0.002 TYR A1382 PHE 0.023 0.002 PHE A 584 TRP 0.013 0.002 TRP A1322 HIS 0.008 0.002 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00459 (13572) covalent geometry : angle 0.60088 (18446) hydrogen bonds : bond 0.03746 ( 840) hydrogen bonds : angle 4.16212 ( 2469) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 168 time to evaluate : 0.651 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.8172 (tpp) cc_final: 0.7862 (ttp) REVERT: A 285 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: A 337 MET cc_start: 0.8617 (tpp) cc_final: 0.8395 (tpp) REVERT: A 350 MET cc_start: 0.8832 (mtp) cc_final: 0.8529 (mtp) REVERT: A 490 ARG cc_start: 0.8435 (mtm-85) cc_final: 0.8115 (tpm170) REVERT: A 542 VAL cc_start: 0.7967 (OUTLIER) cc_final: 0.7596 (p) REVERT: A 551 THR cc_start: 0.7797 (OUTLIER) cc_final: 0.7455 (p) REVERT: A 577 ASP cc_start: 0.7986 (m-30) cc_final: 0.7760 (m-30) REVERT: A 1193 MET cc_start: 0.8036 (mmm) cc_final: 0.7822 (mmm) REVERT: B 276 ASP cc_start: 0.7688 (m-30) cc_final: 0.6850 (p0) REVERT: B 280 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8093 (tm-30) REVERT: B 281 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6582 (mp0) outliers start: 50 outliers final: 19 residues processed: 204 average time/residue: 1.0874 time to fit residues: 246.7485 Evaluate side-chains 156 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1183 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1400 PHE Chi-restraints excluded: chain A residue 1413 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 145 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS A 352 ASN A 361 HIS A 554 GLN ** A1046 HIS ** 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 = 0.4286 r_free = 0.4286 target = 0.114510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.097124 restraints weight = 125914.500| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 4.18 r_work: 0.3862 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.6340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13572 Z= 0.144 Angle : 0.551 6.743 18446 Z= 0.279 Chirality : 0.034 0.176 2167 Planarity : 0.004 0.063 2354 Dihedral : 3.348 17.078 1838 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.27 % Allowed : 17.97 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 1.01 (0.21), residues: 1673 helix: 1.48 (0.15), residues: 1172 sheet: -1.79 (1.67), residues: 9 loop : -1.25 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1442 TYR 0.013 0.001 TYR A 537 PHE 0.018 0.002 PHE A1208 TRP 0.009 0.001 TRP A1680 HIS 0.008 0.001 HIS A1262 Details of bonding type rmsd covalent geometry : bond 0.00319 (13572) covalent geometry : angle 0.55060 (18446) hydrogen bonds : bond 0.03482 ( 840) hydrogen bonds : angle 3.98810 ( 2469) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.635 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: 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 13 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8451 (tp) REVERT: A 167 MET cc_start: 0.8378 (tpp) cc_final: 0.8013 (ttp) REVERT: A 315 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7952 (tm-30) REVERT: A 337 MET cc_start: 0.8575 (tpp) cc_final: 0.8342 (tpp) REVERT: A 490 ARG cc_start: 0.8430 (mtm-85) cc_final: 0.8086 (tpm170) REVERT: A 542 VAL cc_start: 0.7913 (OUTLIER) cc_final: 0.7671 (p) REVERT: A 551 THR cc_start: 0.7778 (OUTLIER) cc_final: 0.7494 (p) REVERT: A 861 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7225 (mt) REVERT: B 264 ILE cc_start: 0.9256 (tt) cc_final: 0.9003 (pp) REVERT: B 269 GLU cc_start: 0.8137 (pp20) cc_final: 0.7909 (pp20) REVERT: B 280 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8109 (tm-30) REVERT: B 281 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6546 (mp0) outliers start: 32 outliers final: 14 residues processed: 174 average time/residue: 0.9967 time to fit residues: 194.6116 Evaluate side-chains 153 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1258 MET Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1400 PHE Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1413 GLU Chi-restraints excluded: chain A residue 1719 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 160 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.114553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.097450 restraints weight = 125798.325| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 4.11 r_work: 0.3866 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3874 r_free = 0.3874 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3874 r_free = 0.3874 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.6563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13572 Z= 0.129 Angle : 0.551 8.049 18446 Z= 0.274 Chirality : 0.034 0.180 2167 Planarity : 0.004 0.061 2354 Dihedral : 3.290 15.696 1838 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.41 % Allowed : 18.11 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 1.14 (0.21), residues: 1673 helix: 1.56 (0.15), residues: 1175 sheet: -1.36 (1.80), residues: 9 loop : -1.16 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 270 TYR 0.011 0.001 TYR A 828 PHE 0.038 0.001 PHE A1208 TRP 0.008 0.001 TRP A1680 HIS 0.013 0.001 HIS A1262 Details of bonding type rmsd covalent geometry : bond 0.00291 (13572) covalent geometry : angle 0.55055 (18446) hydrogen bonds : bond 0.03352 ( 840) hydrogen bonds : angle 3.91498 ( 2469) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.416 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: 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 13 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8439 (tp) REVERT: A 167 MET cc_start: 0.8400 (tpp) cc_final: 0.8059 (ttp) REVERT: A 191 SER cc_start: 0.8445 (m) cc_final: 0.7984 (p) REVERT: A 315 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7938 (tm-30) REVERT: A 337 MET cc_start: 0.8598 (tpp) cc_final: 0.8360 (tpp) REVERT: A 365 TYR cc_start: 0.6945 (t80) cc_final: 0.6164 (t80) REVERT: A 370 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8648 (mm-30) REVERT: A 490 ARG cc_start: 0.8419 (mtm-85) cc_final: 0.8081 (tpm170) REVERT: A 542 VAL cc_start: 0.7950 (OUTLIER) cc_final: 0.7669 (p) REVERT: A 551 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7510 (p) REVERT: B 264 ILE cc_start: 0.9238 (tt) cc_final: 0.8971 (pp) REVERT: B 269 GLU cc_start: 0.8259 (pp20) cc_final: 0.7928 (pp20) REVERT: B 280 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8001 (tm-30) REVERT: B 281 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6051 (mp0) outliers start: 34 outliers final: 12 residues processed: 175 average time/residue: 0.9703 time to fit residues: 190.8052 Evaluate side-chains 156 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1183 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1400 PHE Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1413 GLU Chi-restraints excluded: chain A residue 1719 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 148 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 161 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.112127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.094633 restraints weight = 126257.920| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 4.09 r_work: 0.3809 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3818 r_free = 0.3818 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3818 r_free = 0.3818 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.7032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13572 Z= 0.175 Angle : 0.578 7.859 18446 Z= 0.294 Chirality : 0.035 0.175 2167 Planarity : 0.004 0.059 2354 Dihedral : 3.416 16.505 1838 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.41 % Allowed : 18.54 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 1.07 (0.21), residues: 1673 helix: 1.55 (0.15), residues: 1166 sheet: -1.20 (1.83), residues: 9 loop : -1.28 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 270 TYR 0.019 0.002 TYR A 537 PHE 0.032 0.002 PHE A1208 TRP 0.010 0.001 TRP A1680 HIS 0.014 0.001 HIS A1262 Details of bonding type rmsd covalent geometry : bond 0.00384 (13572) covalent geometry : angle 0.57752 (18446) hydrogen bonds : bond 0.03584 ( 840) hydrogen bonds : angle 4.02507 ( 2469) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.650 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: 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 13 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8466 (tp) REVERT: A 67 GLU cc_start: 0.7801 (tt0) cc_final: 0.7265 (tm-30) REVERT: A 191 SER cc_start: 0.8474 (m) cc_final: 0.8122 (p) REVERT: A 337 MET cc_start: 0.8625 (tpp) cc_final: 0.8383 (tpp) REVERT: A 490 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.8096 (tpm170) REVERT: A 542 VAL cc_start: 0.8155 (OUTLIER) cc_final: 0.7921 (p) REVERT: A 1409 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: A 1451 ARG cc_start: 0.8075 (mmt180) cc_final: 0.7810 (mmt180) REVERT: B 264 ILE cc_start: 0.9273 (tt) cc_final: 0.8997 (pp) REVERT: B 269 GLU cc_start: 0.8317 (pp20) cc_final: 0.8035 (pp20) REVERT: B 280 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8147 (tm-30) outliers start: 34 outliers final: 14 residues processed: 174 average time/residue: 0.9719 time to fit residues: 190.1326 Evaluate side-chains 152 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1183 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1400 PHE Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1413 GLU Chi-restraints excluded: chain A residue 1719 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 91 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 158 optimal weight: 0.0980 chunk 133 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.113327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.095625 restraints weight = 127038.526| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 4.18 r_work: 0.3826 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3834 r_free = 0.3834 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3834 r_free = 0.3834 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.7097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13572 Z= 0.119 Angle : 0.547 7.607 18446 Z= 0.273 Chirality : 0.034 0.176 2167 Planarity : 0.004 0.062 2354 Dihedral : 3.341 16.048 1838 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.78 % Allowed : 19.74 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 1.29 (0.21), residues: 1673 helix: 1.69 (0.15), residues: 1173 sheet: -0.76 (2.01), residues: 9 loop : -1.18 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 270 TYR 0.011 0.001 TYR A 828 PHE 0.024 0.001 PHE A1208 TRP 0.012 0.001 TRP A1380 HIS 0.012 0.001 HIS A1262 Details of bonding type rmsd covalent geometry : bond 0.00266 (13572) covalent geometry : angle 0.54704 (18446) hydrogen bonds : bond 0.03333 ( 840) hydrogen bonds : angle 3.87146 ( 2469) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.552 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: 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 13 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8421 (tp) REVERT: A 191 SER cc_start: 0.8392 (m) cc_final: 0.8068 (p) REVERT: A 337 MET cc_start: 0.8618 (tpp) cc_final: 0.8380 (tpp) REVERT: A 490 ARG cc_start: 0.8344 (mtm-85) cc_final: 0.8072 (tpm170) REVERT: A 542 VAL cc_start: 0.8227 (OUTLIER) cc_final: 0.7641 (p) REVERT: A 546 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8216 (mp) REVERT: A 551 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7528 (p) REVERT: A 597 ASN cc_start: 0.8445 (m110) cc_final: 0.8125 (m-40) REVERT: A 1451 ARG cc_start: 0.8037 (mmt180) cc_final: 0.7791 (mmt180) REVERT: B 264 ILE cc_start: 0.9246 (tt) cc_final: 0.8964 (pp) REVERT: B 269 GLU cc_start: 0.8263 (pp20) cc_final: 0.8040 (pp20) REVERT: B 280 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8165 (tm-30) outliers start: 25 outliers final: 13 residues processed: 160 average time/residue: 0.9363 time to fit residues: 169.7007 Evaluate side-chains 154 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1183 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1400 PHE Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1413 GLU Chi-restraints excluded: chain A residue 1719 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 22 optimal weight: 0.0870 chunk 88 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 135 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.113247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.095500 restraints weight = 126254.332| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 4.19 r_work: 0.3816 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3826 r_free = 0.3826 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3826 r_free = 0.3826 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.7160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13572 Z= 0.120 Angle : 0.554 7.896 18446 Z= 0.275 Chirality : 0.034 0.177 2167 Planarity : 0.004 0.061 2354 Dihedral : 3.319 15.806 1838 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.42 % Allowed : 20.24 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 1.36 (0.21), residues: 1673 helix: 1.73 (0.15), residues: 1175 sheet: -0.57 (2.09), residues: 9 loop : -1.13 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 270 TYR 0.011 0.001 TYR A 828 PHE 0.034 0.001 PHE A1208 TRP 0.009 0.001 TRP A1380 HIS 0.015 0.001 HIS A1262 Details of bonding type rmsd covalent geometry : bond 0.00269 (13572) covalent geometry : angle 0.55402 (18446) hydrogen bonds : bond 0.03280 ( 840) hydrogen bonds : angle 3.83751 ( 2469) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.694 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: 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 13 LEU cc_start: 0.8712 (tp) cc_final: 0.8433 (tp) REVERT: A 67 GLU cc_start: 0.7766 (tt0) cc_final: 0.7309 (tm-30) REVERT: A 191 SER cc_start: 0.8457 (m) cc_final: 0.8054 (p) REVERT: A 337 MET cc_start: 0.8680 (tpp) cc_final: 0.8416 (tpp) REVERT: A 490 ARG cc_start: 0.8373 (mtm-85) cc_final: 0.8060 (tpm170) REVERT: A 542 VAL cc_start: 0.8159 (OUTLIER) cc_final: 0.7862 (p) REVERT: A 551 THR cc_start: 0.7859 (OUTLIER) cc_final: 0.7571 (p) REVERT: A 597 ASN cc_start: 0.8475 (m110) cc_final: 0.8156 (m-40) REVERT: A 1409 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: A 1451 ARG cc_start: 0.8040 (mmt180) cc_final: 0.7790 (mmt180) REVERT: B 264 ILE cc_start: 0.9216 (tt) cc_final: 0.8921 (pp) REVERT: B 280 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8173 (tm-30) outliers start: 20 outliers final: 14 residues processed: 157 average time/residue: 0.9181 time to fit residues: 164.1544 Evaluate side-chains 152 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1183 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1400 PHE Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1413 GLU Chi-restraints excluded: chain A residue 1455 HIS Chi-restraints excluded: chain A residue 1719 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.111416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.093731 restraints weight = 126234.304| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 4.15 r_work: 0.3783 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.7389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13572 Z= 0.164 Angle : 0.575 7.507 18446 Z= 0.292 Chirality : 0.035 0.181 2167 Planarity : 0.004 0.060 2354 Dihedral : 3.422 16.201 1838 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.42 % Allowed : 20.53 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 1.20 (0.21), residues: 1673 helix: 1.61 (0.15), residues: 1178 sheet: -0.69 (2.07), residues: 9 loop : -1.20 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 270 TYR 0.013 0.001 TYR A 537 PHE 0.030 0.002 PHE A1208 TRP 0.010 0.001 TRP A1680 HIS 0.014 0.001 HIS A1262 Details of bonding type rmsd covalent geometry : bond 0.00359 (13572) covalent geometry : angle 0.57527 (18446) hydrogen bonds : bond 0.03489 ( 840) hydrogen bonds : angle 3.94506 ( 2469) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.554 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8707 (tp) cc_final: 0.8416 (tp) REVERT: A 167 MET cc_start: 0.7279 (ttp) cc_final: 0.7071 (ttp) REVERT: A 191 SER cc_start: 0.8519 (m) cc_final: 0.8162 (p) REVERT: A 337 MET cc_start: 0.8695 (tpp) cc_final: 0.8432 (tpp) REVERT: A 490 ARG cc_start: 0.8385 (mtm-85) cc_final: 0.8087 (tpm170) REVERT: A 542 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.7916 (p) REVERT: A 597 ASN cc_start: 0.8493 (m110) cc_final: 0.8172 (m-40) REVERT: A 1175 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.7061 (mpp) REVERT: A 1232 MET cc_start: 0.7583 (tpp) cc_final: 0.7295 (tpp) REVERT: A 1409 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: A 1451 ARG cc_start: 0.8137 (mmt180) cc_final: 0.7861 (mmt180) REVERT: A 1659 MET cc_start: 0.8126 (ttt) cc_final: 0.7707 (tmm) REVERT: B 264 ILE cc_start: 0.9252 (tt) cc_final: 0.8961 (pp) REVERT: B 280 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8189 (tm-30) outliers start: 20 outliers final: 12 residues processed: 152 average time/residue: 0.8925 time to fit residues: 154.4215 Evaluate side-chains 148 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1175 MET Chi-restraints excluded: chain A residue 1183 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1400 PHE Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1413 GLU Chi-restraints excluded: chain A residue 1719 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 30 optimal weight: 2.9990 chunk 64 optimal weight: 0.0980 chunk 56 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 99 optimal weight: 0.0970 chunk 79 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.112495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.094746 restraints weight = 125340.548| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 4.15 r_work: 0.3804 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.7433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13572 Z= 0.116 Angle : 0.554 7.013 18446 Z= 0.276 Chirality : 0.034 0.180 2167 Planarity : 0.004 0.061 2354 Dihedral : 3.365 15.811 1838 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.21 % Allowed : 20.95 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 1.37 (0.21), residues: 1673 helix: 1.73 (0.15), residues: 1177 sheet: -0.48 (2.21), residues: 9 loop : -1.11 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 270 TYR 0.011 0.001 TYR A 828 PHE 0.026 0.001 PHE A1208 TRP 0.009 0.001 TRP A1680 HIS 0.012 0.001 HIS A1262 Details of bonding type rmsd covalent geometry : bond 0.00261 (13572) covalent geometry : angle 0.55356 (18446) hydrogen bonds : bond 0.03276 ( 840) hydrogen bonds : angle 3.82101 ( 2469) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8169.46 seconds wall clock time: 138 minutes 41.51 seconds (8321.51 seconds total)