Starting phenix.real_space_refine on Sun May 25 18:36:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mvz_24059/05_2025/7mvz_24059.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mvz_24059/05_2025/7mvz_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_24059/05_2025/7mvz_24059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mvz_24059/05_2025/7mvz_24059.map" model { file = "/net/cci-nas-00/data/ceres_data/7mvz_24059/05_2025/7mvz_24059.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mvz_24059/05_2025/7mvz_24059.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.45, per 1000 atoms: 0.43 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: 6.79 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 4.26 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: 14.95 Time building geometry restraints manager: 8.19 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.420 Extract box with map and model: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 61.340 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.080 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:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.270 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.005 0.001 TRP A1205 HIS 0.001 0.000 HIS A 211 PHE 0.015 0.001 PHE B 278 TYR 0.018 0.001 TYR A 533 ARG 0.006 0.000 ARG A1325 Details of bonding type rmsd hydrogen bonds : bond 0.12453 ( 840) hydrogen bonds : angle 5.17551 ( 2469) covalent geometry : bond 0.00202 (13572) covalent geometry : angle 0.47799 (18446) *********************** 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 : 1.985 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: 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: 2.2761 time to fit residues: 1003.4255 Evaluate side-chains 201 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 1.869 ------------------------------------------------------------------------------- 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 143 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 0.0370 chunk 133 optimal weight: 0.0870 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN A 492 GLN A 652 ASN ** A1510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.125524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.108694 restraints weight = 127436.475| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 4.28 r_work: 0.4086 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4098 r_free = 0.4098 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 = 0.4098 r_free = 0.4098 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13572 Z= 0.157 Angle : 0.563 6.132 18446 Z= 0.289 Chirality : 0.035 0.146 2167 Planarity : 0.005 0.084 2354 Dihedral : 3.101 42.354 1841 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.84 % Allowed : 13.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.21), residues: 1673 helix: 0.90 (0.15), residues: 1154 sheet: -2.76 (1.21), residues: 9 loop : -1.38 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1138 HIS 0.003 0.001 HIS A 288 PHE 0.021 0.002 PHE A1581 TYR 0.014 0.001 TYR A1008 ARG 0.005 0.000 ARG A1013 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 840) hydrogen bonds : angle 4.13335 ( 2469) covalent geometry : bond 0.00345 (13572) covalent geometry : angle 0.56272 (18446) *********************** 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: 40 poor density : 189 time to evaluate : 1.896 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: A 167 MET cc_start: 0.7889 (tpp) cc_final: 0.7654 (ttp) REVERT: A 211 HIS cc_start: 0.7665 (t-170) cc_final: 0.7318 (t-90) REVERT: A 350 MET cc_start: 0.8706 (mtp) cc_final: 0.8444 (mtp) REVERT: A 387 THR cc_start: 0.8039 (m) cc_final: 0.7829 (p) REVERT: A 490 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.8090 (tpm170) REVERT: A 578 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8209 (pp20) REVERT: A 1320 THR cc_start: 0.7367 (OUTLIER) cc_final: 0.7109 (m) REVERT: A 1680 TRP cc_start: 0.7459 (t60) cc_final: 0.7229 (t60) REVERT: B 276 ASP cc_start: 0.7487 (m-30) cc_final: 0.6850 (p0) REVERT: B 280 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8159 (pp20) outliers start: 40 outliers final: 19 residues processed: 223 average time/residue: 2.3639 time to fit residues: 585.9965 Evaluate side-chains 179 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 1.874 ------------------------------------------------------------------------------- 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 351 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 1183 SER Chi-restraints excluded: chain A residue 1207 ILE 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 1847 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 11 optimal weight: 2.9990 chunk 120 optimal weight: 0.3980 chunk 60 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 88 optimal weight: 0.3980 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 377 GLN A 471 GLN A1510 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.124676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.107657 restraints weight = 127151.094| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 4.30 r_work: 0.4069 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4081 r_free = 0.4081 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4081 r_free = 0.4081 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.4354 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= 0.113 Angle : 0.511 5.695 18446 Z= 0.256 Chirality : 0.033 0.138 2167 Planarity : 0.004 0.068 2354 Dihedral : 2.803 11.247 1838 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.20 % Allowed : 15.48 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.21), residues: 1673 helix: 1.36 (0.16), residues: 1156 sheet: -2.11 (1.52), residues: 9 loop : -1.25 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1380 HIS 0.004 0.001 HIS A 815 PHE 0.014 0.001 PHE A 581 TYR 0.009 0.001 TYR A 828 ARG 0.006 0.000 ARG A1267 Details of bonding type rmsd hydrogen bonds : bond 0.03194 ( 840) hydrogen bonds : angle 3.86115 ( 2469) covalent geometry : bond 0.00254 (13572) covalent geometry : angle 0.51124 (18446) *********************** 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 195 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 1.963 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: A 167 MET cc_start: 0.7942 (tpp) cc_final: 0.7656 (ttp) REVERT: A 211 HIS cc_start: 0.7629 (t-170) cc_final: 0.7257 (t-90) REVERT: A 350 MET cc_start: 0.8724 (mtp) cc_final: 0.8466 (mtp) REVERT: A 365 TYR cc_start: 0.6610 (t80) cc_final: 0.6362 (t80) REVERT: A 370 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8312 (mm-30) REVERT: A 490 ARG cc_start: 0.8349 (mtm-85) cc_final: 0.8024 (tpm170) REVERT: A 551 THR cc_start: 0.7918 (OUTLIER) cc_final: 0.7684 (p) REVERT: A 578 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8181 (pp20) REVERT: A 1320 THR cc_start: 0.7398 (OUTLIER) cc_final: 0.7127 (m) REVERT: B 276 ASP cc_start: 0.7505 (m-30) cc_final: 0.6760 (p0) REVERT: B 280 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8081 (pp20) outliers start: 31 outliers final: 9 residues processed: 187 average time/residue: 2.2941 time to fit residues: 481.6991 Evaluate side-chains 158 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 551 THR 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 1459 LEU Chi-restraints excluded: chain A residue 1475 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.7302 > 50: distance: 73 - 115: 20.874 distance: 89 - 131: 18.263 distance: 100 - 143: 25.604 distance: 107 - 115: 21.044 distance: 108 - 153: 31.826 distance: 115 - 116: 11.405 distance: 115 - 122: 12.171 distance: 116 - 117: 23.961 distance: 116 - 119: 7.351 distance: 116 - 123: 42.746 distance: 117 - 118: 18.204 distance: 117 - 131: 20.651 distance: 118 - 172: 27.638 distance: 119 - 120: 19.949 distance: 119 - 121: 36.076 distance: 119 - 124: 31.533 distance: 120 - 125: 34.083 distance: 120 - 126: 22.803 distance: 120 - 127: 23.392 distance: 121 - 128: 14.493 distance: 121 - 129: 28.183 distance: 121 - 130: 9.603 distance: 131 - 132: 15.377 distance: 131 - 139: 32.248 distance: 132 - 133: 9.773 distance: 132 - 135: 10.703 distance: 132 - 140: 5.112 distance: 133 - 134: 8.511 distance: 133 - 143: 11.773 distance: 134 - 188: 43.316 distance: 135 - 141: 10.019 distance: 135 - 142: 56.812 distance: 136 - 138: 46.354 distance: 143 - 144: 5.738 distance: 143 - 148: 38.625 distance: 144 - 147: 35.425 distance: 144 - 149: 36.213 distance: 145 - 146: 10.304 distance: 145 - 153: 5.510 distance: 146 - 202: 36.445 distance: 147 - 150: 48.696 distance: 153 - 154: 22.369 distance: 153 - 161: 7.205 distance: 154 - 155: 12.127 distance: 154 - 157: 3.212 distance: 154 - 162: 5.530 distance: 155 - 156: 7.201 distance: 155 - 172: 25.863 distance: 156 - 222: 58.315 distance: 157 - 158: 25.094 distance: 157 - 163: 16.180 distance: 157 - 164: 17.877 distance: 158 - 159: 20.187 distance: 158 - 160: 13.908 distance: 158 - 165: 11.023 distance: 159 - 168: 9.536 distance: 160 - 169: 24.902 distance: 160 - 170: 31.439 distance: 160 - 171: 9.306 distance: 172 - 173: 46.963 distance: 172 - 179: 31.230 distance: 173 - 174: 40.211 distance: 173 - 176: 18.476 distance: 173 - 180: 12.857 distance: 174 - 188: 11.886 distance: 175 - 241: 39.341 distance: 176 - 177: 37.391 distance: 176 - 178: 8.966 distance: 176 - 181: 14.940 distance: 177 - 182: 4.608 distance: 177 - 184: 3.978 distance: 178 - 185: 13.427 distance: 178 - 186: 15.454 distance: 178 - 187: 39.899 distance: 188 - 189: 19.381 distance: 188 - 195: 28.778 distance: 189 - 190: 22.416 distance: 189 - 192: 41.810 distance: 189 - 196: 11.249 distance: 190 - 191: 19.887 distance: 190 - 202: 28.342 distance: 191 - 260: 40.964 distance: 192 - 194: 35.086 distance: 192 - 197: 40.570 distance: 193 - 198: 15.801 distance: 194 - 199: 10.273 distance: 194 - 200: 3.886 distance: 194 - 201: 39.680 distance: 202 - 203: 21.062 distance: 202 - 213: 9.595 distance: 203 - 204: 24.325 distance: 203 - 206: 17.480 distance: 203 - 214: 10.938 distance: 204 - 205: 48.972 distance: 204 - 222: 11.369 distance: 206 - 207: 27.804 distance: 206 - 216: 38.635 distance: 207 - 208: 11.677 distance: 207 - 209: 42.007 distance: 208 - 210: 39.062 distance: 222 - 223: 27.841 distance: 223 - 224: 15.697 distance: 223 - 226: 47.531 distance: 223 - 231: 53.450 distance: 224 - 225: 56.585 distance: 226 - 227: 28.272 distance: 226 - 232: 33.521 distance: 226 - 233: 7.028 distance: 227 - 229: 12.953 distance: 228 - 235: 7.919 distance: 228 - 236: 16.444 distance: 228 - 237: 10.524 distance: 229 - 238: 39.867 distance: 229 - 239: 39.962 distance: 229 - 240: 40.402 distance: 241 - 242: 37.097 distance: 242 - 243: 29.565 distance: 242 - 245: 28.021 distance: 242 - 250: 42.284 distance: 243 - 260: 9.357 distance: 245 - 246: 4.338 distance: 246 - 247: 40.536 distance: 246 - 248: 44.300 distance: 247 - 254: 26.274 distance: 247 - 255: 6.721 distance: 248 - 257: 16.460 distance: 248 - 258: 5.640 distance: 248 - 259: 11.475 distance: 260 - 261: 29.785 distance: 260 - 270: 25.754 distance: 261 - 262: 39.134 distance: 261 - 264: 25.637 distance: 262 - 263: 4.051 distance: 262 - 277: 33.672 distance: 264 - 265: 14.731 distance: 264 - 272: 22.459 distance: 265 - 266: 22.879 distance: 265 - 267: 24.866 distance: 266 - 268: 22.637 distance: 267 - 269: 16.140 distance: 267 - 274: 16.490 distance: 268 - 269: 40.808