Starting phenix.real_space_refine on Wed Jun 25 14:41:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7otp_13064/06_2025/7otp_13064.cif Found real_map, /net/cci-nas-00/data/ceres_data/7otp_13064/06_2025/7otp_13064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7otp_13064/06_2025/7otp_13064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7otp_13064/06_2025/7otp_13064.map" model { file = "/net/cci-nas-00/data/ceres_data/7otp_13064/06_2025/7otp_13064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7otp_13064/06_2025/7otp_13064.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 192 5.16 5 C 18616 2.51 5 N 4907 2.21 5 O 5319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.39s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29039 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 28906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3636, 28906 Classifications: {'peptide': 3636} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 158, 'TRANS': 3477} Chain breaks: 16 Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 117 Chain: "A" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 133 Unusual residues: {' MG': 2, 'AGS': 1} Classifications: {'peptide': 20, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 19, None: 3} Not linked: pdbres="UNK A6020 " pdbres="AGS A6101 " Not linked: pdbres="AGS A6101 " pdbres=" MG A6102 " Not linked: pdbres=" MG A6102 " pdbres=" MG A6103 " Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 15.82, per 1000 atoms: 0.54 Number of scatterers: 29039 At special positions: 0 Unit cell: (126.488, 152.568, 182.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 3 15.00 Mg 2 11.99 O 5319 8.00 N 4907 7.00 C 18616 6.00 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: 7.87 Conformation dependent library (CDL) restraints added in 3.8 seconds 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7012 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 6 sheets defined 72.4% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.07 Creating SS restraints... Processing helix chain 'A' and resid 9 through 24 removed outlier: 3.662A pdb=" N LEU A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG A 14 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 24 " --> pdb=" O SER A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 45 removed outlier: 3.522A pdb=" N VAL A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 58 removed outlier: 5.577A pdb=" N THR A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 71 removed outlier: 3.750A pdb=" N ASP A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 97 removed outlier: 3.613A pdb=" N CYS A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 85 " --> pdb=" O CYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 118 removed outlier: 4.351A pdb=" N THR A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 146 removed outlier: 3.918A pdb=" N LYS A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N MET A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 161 removed outlier: 4.197A pdb=" N ALA A 161 " --> pdb=" O TYR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.997A pdb=" N LEU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 185 removed outlier: 4.165A pdb=" N GLY A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 removed outlier: 4.365A pdb=" N PHE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 4.362A pdb=" N CYS A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 removed outlier: 3.863A pdb=" N LEU A 227 " --> pdb=" O CYS A 223 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 4.283A pdb=" N SER A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.941A pdb=" N ASP A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 262' Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 289 through 303 removed outlier: 3.728A pdb=" N LEU A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 330 removed outlier: 3.749A pdb=" N ASN A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 351 Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 369 through 377 Processing helix chain 'A' and resid 380 through 397 removed outlier: 3.587A pdb=" N CYS A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 409 through 423 removed outlier: 4.071A pdb=" N TYR A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 452 through 469 removed outlier: 4.068A pdb=" N VAL A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 492 removed outlier: 4.370A pdb=" N ARG A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 526 Processing helix chain 'A' and resid 527 through 535 Processing helix chain 'A' and resid 539 through 545 Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 559 through 577 Processing helix chain 'A' and resid 616 through 634 removed outlier: 3.538A pdb=" N PHE A 620 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 658 Processing helix chain 'A' and resid 663 through 679 removed outlier: 4.225A pdb=" N TYR A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 718 removed outlier: 3.527A pdb=" N LYS A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 724 through 734 Processing helix chain 'A' and resid 737 through 760 removed outlier: 4.466A pdb=" N LEU A 743 " --> pdb=" O ASN A 739 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP A 744 " --> pdb=" O ILE A 740 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG A 746 " --> pdb=" O GLU A 742 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA A 747 " --> pdb=" O LEU A 743 " (cutoff:3.500A) Proline residue: A 750 - end of helix removed outlier: 3.986A pdb=" N LEU A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 780 removed outlier: 3.810A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 786 Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 796 through 802 removed outlier: 3.784A pdb=" N LEU A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 805 No H-bonds generated for 'chain 'A' and resid 803 through 805' Processing helix chain 'A' and resid 848 through 862 Processing helix chain 'A' and resid 866 through 871 Processing helix chain 'A' and resid 872 through 877 Processing helix chain 'A' and resid 910 through 921 removed outlier: 4.863A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 946 removed outlier: 3.830A pdb=" N THR A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 removed outlier: 4.219A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix removed outlier: 3.558A pdb=" N CYS A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 996 Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 1002 through 1006 Processing helix chain 'A' and resid 1007 through 1012 Processing helix chain 'A' and resid 1023 through 1043 removed outlier: 3.568A pdb=" N GLY A1030 " --> pdb=" O ARG A1026 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A1031 " --> pdb=" O ASP A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1050 removed outlier: 4.200A pdb=" N GLU A1050 " --> pdb=" O PRO A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1071 through 1080 removed outlier: 3.670A pdb=" N ARG A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A1076 " --> pdb=" O ALA A1072 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A1078 " --> pdb=" O LYS A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1086 removed outlier: 3.571A pdb=" N TYR A1086 " --> pdb=" O PHE A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1114 removed outlier: 3.785A pdb=" N GLN A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLU A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1141 Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'A' and resid 1164 through 1175 Processing helix chain 'A' and resid 1180 through 1195 Processing helix chain 'A' and resid 1196 through 1198 No H-bonds generated for 'chain 'A' and resid 1196 through 1198' Processing helix chain 'A' and resid 1203 through 1215 Processing helix chain 'A' and resid 1217 through 1226 Processing helix chain 'A' and resid 1251 through 1272 Processing helix chain 'A' and resid 1277 through 1282 removed outlier: 3.850A pdb=" N VAL A1281 " --> pdb=" O GLY A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1298 Processing helix chain 'A' and resid 1323 through 1325 No H-bonds generated for 'chain 'A' and resid 1323 through 1325' Processing helix chain 'A' and resid 1326 through 1351 removed outlier: 3.577A pdb=" N SER A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1353 through 1361 removed outlier: 3.717A pdb=" N LYS A1357 " --> pdb=" O PRO A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1378 removed outlier: 4.134A pdb=" N ARG A1370 " --> pdb=" O THR A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1383 removed outlier: 3.654A pdb=" N GLY A1383 " --> pdb=" O ALA A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1409 Proline residue: A1396 - end of helix removed outlier: 3.528A pdb=" N ASN A1401 " --> pdb=" O ASP A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1423 removed outlier: 3.639A pdb=" N LYS A1422 " --> pdb=" O HIS A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1433 removed outlier: 3.518A pdb=" N ALA A1433 " --> pdb=" O GLU A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1462 Processing helix chain 'A' and resid 1463 through 1468 Processing helix chain 'A' and resid 1476 through 1487 removed outlier: 3.778A pdb=" N GLU A1482 " --> pdb=" O SER A1478 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A1484 " --> pdb=" O GLY A1480 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A1487 " --> pdb=" O LEU A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1520 Processing helix chain 'A' and resid 1524 through 1533 removed outlier: 3.586A pdb=" N SER A1530 " --> pdb=" O GLU A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1563 Processing helix chain 'A' and resid 1563 through 1574 removed outlier: 4.090A pdb=" N ASN A1568 " --> pdb=" O SER A1564 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A1570 " --> pdb=" O THR A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1584 removed outlier: 4.585A pdb=" N LEU A1580 " --> pdb=" O ASP A1576 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1607 Processing helix chain 'A' and resid 1611 through 1625 Processing helix chain 'A' and resid 1626 through 1633 removed outlier: 3.792A pdb=" N ASP A1630 " --> pdb=" O LYS A1627 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER A1631 " --> pdb=" O LYS A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1656 removed outlier: 3.849A pdb=" N ASP A1656 " --> pdb=" O ILE A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1681 Processing helix chain 'A' and resid 1685 through 1693 Processing helix chain 'A' and resid 1696 through 1701 removed outlier: 4.594A pdb=" N SER A1701 " --> pdb=" O PRO A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1706 through 1722 removed outlier: 3.930A pdb=" N LEU A1710 " --> pdb=" O SER A1706 " (cutoff:3.500A) Processing helix chain 'A' and resid 1733 through 1754 Processing helix chain 'A' and resid 1755 through 1768 Processing helix chain 'A' and resid 1774 through 1786 Processing helix chain 'A' and resid 1790 through 1806 Processing helix chain 'A' and resid 1813 through 1822 removed outlier: 3.644A pdb=" N SER A1818 " --> pdb=" O PHE A1814 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1829 Processing helix chain 'A' and resid 1834 through 1854 removed outlier: 3.853A pdb=" N GLU A1838 " --> pdb=" O ASP A1834 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A1848 " --> pdb=" O VAL A1844 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N SER A1853 " --> pdb=" O ASP A1849 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG A1854 " --> pdb=" O VAL A1850 " (cutoff:3.500A) Processing helix chain 'A' and resid 1863 through 1882 Processing helix chain 'A' and resid 1885 through 1889 removed outlier: 3.737A pdb=" N ASP A1888 " --> pdb=" O PRO A1885 " (cutoff:3.500A) Processing helix chain 'A' and resid 1910 through 1924 removed outlier: 3.546A pdb=" N THR A1914 " --> pdb=" O GLU A1910 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA A1922 " --> pdb=" O LEU A1918 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1956 removed outlier: 3.920A pdb=" N CYS A1954 " --> pdb=" O SER A1950 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2106 Processing helix chain 'A' and resid 2123 through 2135 removed outlier: 3.868A pdb=" N LEU A2129 " --> pdb=" O TRP A2125 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS A2132 " --> pdb=" O PHE A2128 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2153 removed outlier: 3.819A pdb=" N ARG A2143 " --> pdb=" O PRO A2139 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2158 Processing helix chain 'A' and resid 2160 through 2172 removed outlier: 4.451A pdb=" N SER A2166 " --> pdb=" O LYS A2162 " (cutoff:3.500A) Proline residue: A2167 - end of helix Processing helix chain 'A' and resid 2183 through 2196 Processing helix chain 'A' and resid 2205 through 2222 removed outlier: 3.745A pdb=" N ARG A2214 " --> pdb=" O VAL A2210 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2245 Processing helix chain 'A' and resid 2254 through 2261 Processing helix chain 'A' and resid 2270 through 2283 removed outlier: 3.604A pdb=" N ASN A2283 " --> pdb=" O ILE A2279 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2305 removed outlier: 4.351A pdb=" N TYR A2299 " --> pdb=" O GLN A2295 " (cutoff:3.500A) Processing helix chain 'A' and resid 2306 through 2309 Processing helix chain 'A' and resid 2313 through 2332 removed outlier: 4.491A pdb=" N ALA A2319 " --> pdb=" O VAL A2315 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU A2332 " --> pdb=" O ARG A2328 " (cutoff:3.500A) Processing helix chain 'A' and resid 2337 through 2353 removed outlier: 3.791A pdb=" N HIS A2352 " --> pdb=" O GLN A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2369 removed outlier: 3.544A pdb=" N ILE A2361 " --> pdb=" O GLU A2357 " (cutoff:3.500A) Processing helix chain 'A' and resid 2371 through 2377 removed outlier: 3.932A pdb=" N LEU A2374 " --> pdb=" O PHE A2371 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP A2376 " --> pdb=" O PRO A2373 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG A2377 " --> pdb=" O LEU A2374 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2386 Processing helix chain 'A' and resid 2387 through 2389 No H-bonds generated for 'chain 'A' and resid 2387 through 2389' Processing helix chain 'A' and resid 2391 through 2403 removed outlier: 3.607A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) Processing helix chain 'A' and resid 2412 through 2418 Processing helix chain 'A' and resid 2419 through 2424 removed outlier: 3.953A pdb=" N VAL A2423 " --> pdb=" O ASP A2419 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET A2424 " --> pdb=" O PHE A2420 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2419 through 2424' Processing helix chain 'A' and resid 2428 through 2443 Processing helix chain 'A' and resid 2444 through 2446 No H-bonds generated for 'chain 'A' and resid 2444 through 2446' Processing helix chain 'A' and resid 2447 through 2459 removed outlier: 3.908A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix Processing helix chain 'A' and resid 2460 through 2462 No H-bonds generated for 'chain 'A' and resid 2460 through 2462' Processing helix chain 'A' and resid 2469 through 2484 removed outlier: 3.892A pdb=" N ASN A2475 " --> pdb=" O GLU A2471 " (cutoff:3.500A) Processing helix chain 'A' and resid 2496 through 2509 Processing helix chain 'A' and resid 2510 through 2512 No H-bonds generated for 'chain 'A' and resid 2510 through 2512' Processing helix chain 'A' and resid 2514 through 2526 Processing helix chain 'A' and resid 2534 through 2544 removed outlier: 3.735A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER A2544 " --> pdb=" O LEU A2540 " (cutoff:3.500A) Processing helix chain 'A' and resid 2545 through 2546 No H-bonds generated for 'chain 'A' and resid 2545 through 2546' Processing helix chain 'A' and resid 2547 through 2551 removed outlier: 3.501A pdb=" N GLU A2551 " --> pdb=" O PRO A2548 " (cutoff:3.500A) Processing helix chain 'A' and resid 2557 through 2564 Processing helix chain 'A' and resid 2565 through 2567 No H-bonds generated for 'chain 'A' and resid 2565 through 2567' Processing helix chain 'A' and resid 2787 through 2799 Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2801 through 2820 Processing helix chain 'A' and resid 2821 through 2823 No H-bonds generated for 'chain 'A' and resid 2821 through 2823' Processing helix chain 'A' and resid 2825 through 2847 Processing helix chain 'A' and resid 2851 through 2865 removed outlier: 3.768A pdb=" N GLN A2864 " --> pdb=" O ASP A2860 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS A2865 " --> pdb=" O ILE A2861 " (cutoff:3.500A) Processing helix chain 'A' and resid 2866 through 2869 Processing helix chain 'A' and resid 2872 through 2884 Processing helix chain 'A' and resid 2885 through 2900 removed outlier: 3.835A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2917 through 2934 Processing helix chain 'A' and resid 2935 through 2946 removed outlier: 3.622A pdb=" N SER A2945 " --> pdb=" O GLY A2941 " (cutoff:3.500A) Processing helix chain 'A' and resid 2951 through 2962 removed outlier: 3.686A pdb=" N LEU A2957 " --> pdb=" O THR A2953 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A2962 " --> pdb=" O LEU A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2964 through 2977 removed outlier: 3.877A pdb=" N ASN A2977 " --> pdb=" O ASP A2973 " (cutoff:3.500A) Processing helix chain 'A' and resid 2987 through 3005 removed outlier: 4.000A pdb=" N LEU A2999 " --> pdb=" O GLU A2995 " (cutoff:3.500A) Processing helix chain 'A' and resid 3007 through 3014 removed outlier: 3.694A pdb=" N CYS A3014 " --> pdb=" O SER A3010 " (cutoff:3.500A) Processing helix chain 'A' and resid 3026 through 3031 removed outlier: 3.501A pdb=" N ILE A3030 " --> pdb=" O ASP A3026 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TRP A3031 " --> pdb=" O LEU A3027 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3026 through 3031' Processing helix chain 'A' and resid 3040 through 3054 Processing helix chain 'A' and resid 3059 through 3071 removed outlier: 3.708A pdb=" N THR A3063 " --> pdb=" O GLN A3059 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY A3071 " --> pdb=" O LYS A3067 " (cutoff:3.500A) Processing helix chain 'A' and resid 3075 through 3082 Processing helix chain 'A' and resid 3082 through 3094 removed outlier: 3.760A pdb=" N LEU A3092 " --> pdb=" O LEU A3088 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN A3093 " --> pdb=" O LEU A3089 " (cutoff:3.500A) Processing helix chain 'A' and resid 3095 through 3117 removed outlier: 3.622A pdb=" N ALA A3099 " --> pdb=" O ASP A3095 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A3116 " --> pdb=" O GLN A3112 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A3117 " --> pdb=" O ASN A3113 " (cutoff:3.500A) Processing helix chain 'A' and resid 3121 through 3131 removed outlier: 3.834A pdb=" N SER A3131 " --> pdb=" O THR A3127 " (cutoff:3.500A) Processing helix chain 'A' and resid 3132 through 3146 removed outlier: 4.035A pdb=" N ILE A3138 " --> pdb=" O ALA A3134 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A3139 " --> pdb=" O LEU A3135 " (cutoff:3.500A) Processing helix chain 'A' and resid 3153 through 3166 removed outlier: 4.036A pdb=" N LEU A3157 " --> pdb=" O SER A3153 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A3159 " --> pdb=" O VAL A3155 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3196 removed outlier: 3.547A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A3184 " --> pdb=" O ASP A3180 " (cutoff:3.500A) Processing helix chain 'A' and resid 3230 through 3249 removed outlier: 3.763A pdb=" N PHE A3236 " --> pdb=" O ARG A3232 " (cutoff:3.500A) Processing helix chain 'A' and resid 3253 through 3262 Processing helix chain 'A' and resid 3271 through 3288 removed outlier: 3.764A pdb=" N ARG A3282 " --> pdb=" O GLN A3278 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A3288 " --> pdb=" O SER A3284 " (cutoff:3.500A) Processing helix chain 'A' and resid 3290 through 3307 removed outlier: 4.448A pdb=" N GLU A3295 " --> pdb=" O GLN A3291 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLN A3296 " --> pdb=" O GLY A3292 " (cutoff:3.500A) Processing helix chain 'A' and resid 3322 through 3344 removed outlier: 3.923A pdb=" N GLU A3344 " --> pdb=" O ALA A3340 " (cutoff:3.500A) Processing helix chain 'A' and resid 3345 through 3352 removed outlier: 4.273A pdb=" N LEU A3348 " --> pdb=" O PRO A3345 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A3350 " --> pdb=" O CYS A3347 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU A3352 " --> pdb=" O ALA A3349 " (cutoff:3.500A) Processing helix chain 'A' and resid 3354 through 3364 Processing helix chain 'A' and resid 3369 through 3393 Processing helix chain 'A' and resid 3406 through 3430 removed outlier: 3.584A pdb=" N ILE A3410 " --> pdb=" O ALA A3406 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3456 removed outlier: 3.612A pdb=" N LEU A3456 " --> pdb=" O LYS A3452 " (cutoff:3.500A) Processing helix chain 'A' and resid 3458 through 3465 Processing helix chain 'A' and resid 3465 through 3474 removed outlier: 3.954A pdb=" N LEU A3469 " --> pdb=" O PHE A3465 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A3473 " --> pdb=" O LEU A3469 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A3474 " --> pdb=" O GLN A3470 " (cutoff:3.500A) Processing helix chain 'A' and resid 3475 through 3479 Processing helix chain 'A' and resid 3480 through 3490 removed outlier: 3.537A pdb=" N SER A3489 " --> pdb=" O LYS A3485 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3497 No H-bonds generated for 'chain 'A' and resid 3495 through 3497' Processing helix chain 'A' and resid 3498 through 3506 removed outlier: 4.145A pdb=" N ALA A3504 " --> pdb=" O SER A3500 " (cutoff:3.500A) Processing helix chain 'A' and resid 3514 through 3525 removed outlier: 3.656A pdb=" N ASP A3523 " --> pdb=" O GLU A3519 " (cutoff:3.500A) Processing helix chain 'A' and resid 3529 through 3538 removed outlier: 3.678A pdb=" N GLU A3538 " --> pdb=" O ILE A3534 " (cutoff:3.500A) Processing helix chain 'A' and resid 3547 through 3550 Processing helix chain 'A' and resid 3551 through 3563 Processing helix chain 'A' and resid 3566 through 3576 Processing helix chain 'A' and resid 3580 through 3594 Processing helix chain 'A' and resid 3604 through 3607 Processing helix chain 'A' and resid 3608 through 3617 removed outlier: 4.071A pdb=" N ALA A3616 " --> pdb=" O ARG A3612 " (cutoff:3.500A) Processing helix chain 'A' and resid 3626 through 3636 removed outlier: 3.760A pdb=" N PHE A3632 " --> pdb=" O PHE A3628 " (cutoff:3.500A) Processing helix chain 'A' and resid 3639 through 3644 Processing helix chain 'A' and resid 3649 through 3653 Processing helix chain 'A' and resid 3657 through 3673 removed outlier: 3.612A pdb=" N ASP A3661 " --> pdb=" O SER A3657 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A3672 " --> pdb=" O LEU A3668 " (cutoff:3.500A) Processing helix chain 'A' and resid 3686 through 3690 Processing helix chain 'A' and resid 3758 through 3778 Processing helix chain 'A' and resid 3779 through 3784 removed outlier: 3.763A pdb=" N ARG A3784 " --> pdb=" O ALA A3780 " (cutoff:3.500A) Processing helix chain 'A' and resid 3812 through 3820 removed outlier: 3.888A pdb=" N THR A3819 " --> pdb=" O LEU A3815 " (cutoff:3.500A) Processing helix chain 'A' and resid 3821 through 3830 Processing helix chain 'A' and resid 3834 through 3847 removed outlier: 4.464A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3862 removed outlier: 3.839A pdb=" N LEU A3857 " --> pdb=" O GLY A3853 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS A3860 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3865 through 3878 removed outlier: 3.583A pdb=" N SER A3876 " --> pdb=" O ARG A3872 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS A3877 " --> pdb=" O LYS A3873 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL A3878 " --> pdb=" O ARG A3874 " (cutoff:3.500A) Processing helix chain 'A' and resid 3881 through 3890 removed outlier: 3.572A pdb=" N ARG A3885 " --> pdb=" O ASP A3881 " (cutoff:3.500A) Processing helix chain 'A' and resid 3893 through 3918 removed outlier: 4.269A pdb=" N ALA A3899 " --> pdb=" O GLU A3895 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A3917 " --> pdb=" O ILE A3913 " (cutoff:3.500A) Processing helix chain 'A' and resid 3924 through 3927 Processing helix chain 'A' and resid 3947 through 3952 Processing helix chain 'A' and resid 3964 through 3971 removed outlier: 4.541A pdb=" N MET A3971 " --> pdb=" O PHE A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3978 through 3994 removed outlier: 3.870A pdb=" N MET A3984 " --> pdb=" O MET A3980 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS A3986 " --> pdb=" O SER A3982 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP A3994 " --> pdb=" O ALA A3990 " (cutoff:3.500A) Processing helix chain 'A' and resid 3994 through 4007 removed outlier: 4.306A pdb=" N LEU A3998 " --> pdb=" O ASP A3994 " (cutoff:3.500A) Processing helix chain 'A' and resid 4012 through 4022 removed outlier: 3.627A pdb=" N LYS A4022 " --> pdb=" O GLN A4018 " (cutoff:3.500A) Processing helix chain 'A' and resid 4040 through 4050 removed outlier: 4.629A pdb=" N TYR A4046 " --> pdb=" O GLN A4042 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA A4047 " --> pdb=" O LYS A4043 " (cutoff:3.500A) Processing helix chain 'A' and resid 4055 through 4068 removed outlier: 3.567A pdb=" N LEU A4064 " --> pdb=" O THR A4060 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4083 Processing helix chain 'A' and resid 4101 through 4112 Processing helix chain 'A' and resid 4113 through 4119 removed outlier: 3.784A pdb=" N ARG A4119 " --> pdb=" O ASN A4115 " (cutoff:3.500A) Processing helix chain 'A' and resid 4120 through 4125 removed outlier: 5.923A pdb=" N GLY A4123 " --> pdb=" O THR A4120 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A4125 " --> pdb=" O GLU A4122 " (cutoff:3.500A) Processing helix chain 'A' and resid 6002 through 6016 removed outlier: 3.712A pdb=" N UNK A6008 " --> pdb=" O UNK A6004 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N UNK A6011 " --> pdb=" O UNK A6007 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N UNK A6012 " --> pdb=" O UNK A6008 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N UNK A6013 " --> pdb=" O UNK A6009 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 583 through 585 Processing sheet with id=AA2, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AA3, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 4.173A pdb=" N ARG A3746 " --> pdb=" O GLY A3742 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3727 through 3728 Processing sheet with id=AA5, first strand: chain 'A' and resid 3752 through 3753 removed outlier: 3.760A pdb=" N GLY A3801 " --> pdb=" O LYS A3753 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET A3796 " --> pdb=" O LEU A3800 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 3809 through 3811 1600 hydrogen bonds defined for protein. 4710 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: 15.60 Time building geometry restraints manager: 8.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.38: 10952 1.38 - 1.56: 18370 1.56 - 1.75: 10 1.75 - 1.94: 297 1.94 - 2.13: 1 Bond restraints: 29630 Sorted by residual: bond pdb=" C3' AGS A6101 " pdb=" C4' AGS A6101 " ideal model delta sigma weight residual 1.526 1.334 0.192 1.10e-02 8.26e+03 3.05e+02 bond pdb=" C4' AGS A6101 " pdb=" O4' AGS A6101 " ideal model delta sigma weight residual 1.444 1.635 -0.191 1.20e-02 6.94e+03 2.53e+02 bond pdb=" C6 AGS A6101 " pdb=" N6 AGS A6101 " ideal model delta sigma weight residual 1.335 1.472 -0.137 1.00e-02 1.00e+04 1.88e+02 bond pdb=" C1' AGS A6101 " pdb=" O4' AGS A6101 " ideal model delta sigma weight residual 1.415 1.295 0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" PG AGS A6101 " pdb=" S1G AGS A6101 " ideal model delta sigma weight residual 1.949 2.126 -0.177 2.00e-02 2.50e+03 7.84e+01 ... (remaining 29625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 39019 2.35 - 4.69: 893 4.69 - 7.04: 136 7.04 - 9.38: 23 9.38 - 11.73: 7 Bond angle restraints: 40078 Sorted by residual: angle pdb=" C5 AGS A6101 " pdb=" C4 AGS A6101 " pdb=" N3 AGS A6101 " ideal model delta sigma weight residual 126.80 118.10 8.70 7.41e-01 1.82e+00 1.38e+02 angle pdb=" C5 AGS A6101 " pdb=" N7 AGS A6101 " pdb=" C8 AGS A6101 " ideal model delta sigma weight residual 103.67 108.13 -4.46 4.26e-01 5.51e+00 1.10e+02 angle pdb=" N TYR A3715 " pdb=" CA TYR A3715 " pdb=" C TYR A3715 " ideal model delta sigma weight residual 112.88 101.15 11.73 1.29e+00 6.01e-01 8.27e+01 angle pdb=" N1 AGS A6101 " pdb=" C2 AGS A6101 " pdb=" N3 AGS A6101 " ideal model delta sigma weight residual 128.80 121.75 7.05 8.41e-01 1.41e+00 7.02e+01 angle pdb=" N3 AGS A6101 " pdb=" C4 AGS A6101 " pdb=" N9 AGS A6101 " ideal model delta sigma weight residual 127.16 135.43 -8.27 1.06e+00 8.92e-01 6.09e+01 ... (remaining 40073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.16: 16162 18.16 - 36.32: 1633 36.32 - 54.48: 220 54.48 - 72.64: 39 72.64 - 90.80: 30 Dihedral angle restraints: 18084 sinusoidal: 7327 harmonic: 10757 Sorted by residual: dihedral pdb=" CA ILE A2785 " pdb=" C ILE A2785 " pdb=" N LYS A2786 " pdb=" CA LYS A2786 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA LYS A2445 " pdb=" C LYS A2445 " pdb=" N LEU A2446 " pdb=" CA LEU A2446 " ideal model delta harmonic sigma weight residual 180.00 -152.55 -27.45 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA GLY A4024 " pdb=" C GLY A4024 " pdb=" N GLY A4025 " pdb=" CA GLY A4025 " ideal model delta harmonic sigma weight residual -180.00 -153.75 -26.25 0 5.00e+00 4.00e-02 2.76e+01 ... (remaining 18081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3523 0.055 - 0.111: 929 0.111 - 0.166: 103 0.166 - 0.221: 12 0.221 - 0.276: 3 Chirality restraints: 4570 Sorted by residual: chirality pdb=" CB ILE A4089 " pdb=" CA ILE A4089 " pdb=" CG1 ILE A4089 " pdb=" CG2 ILE A4089 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C3' AGS A6101 " pdb=" C2' AGS A6101 " pdb=" C4' AGS A6101 " pdb=" O3' AGS A6101 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA GLU A3033 " pdb=" N GLU A3033 " pdb=" C GLU A3033 " pdb=" CB GLU A3033 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 4567 not shown) Planarity restraints: 5084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A1238 " -0.103 5.00e-02 4.00e+02 1.52e-01 3.68e+01 pdb=" N PRO A1239 " 0.262 5.00e-02 4.00e+02 pdb=" CA PRO A1239 " -0.082 5.00e-02 4.00e+02 pdb=" CD PRO A1239 " -0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1802 " 0.028 2.00e-02 2.50e+03 2.39e-02 1.14e+01 pdb=" CG TYR A1802 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR A1802 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A1802 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A1802 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR A1802 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A1802 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A1802 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 722 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C LYS A 722 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS A 722 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP A 723 " 0.019 2.00e-02 2.50e+03 ... (remaining 5081 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 358 2.59 - 3.17: 27614 3.17 - 3.75: 46074 3.75 - 4.32: 62833 4.32 - 4.90: 101135 Nonbonded interactions: 238014 Sorted by model distance: nonbonded pdb=" O2G AGS A6101 " pdb="MG MG A6102 " model vdw 2.017 2.170 nonbonded pdb=" O TRP A1632 " pdb=" OG SER A1637 " model vdw 2.068 3.040 nonbonded pdb=" O SER A3288 " pdb=" NH1 ARG A3289 " model vdw 2.119 3.120 nonbonded pdb=" O TYR A 265 " pdb=" OG SER A 269 " model vdw 2.131 3.040 nonbonded pdb=" O1B AGS A6101 " pdb="MG MG A6103 " model vdw 2.145 2.170 ... (remaining 238009 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.95 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: 1.430 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: 0.020 Extract box with map and model: 1.260 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 69.510 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.120 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:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.192 29630 Z= 0.357 Angle : 0.866 11.731 40078 Z= 0.479 Chirality : 0.048 0.276 4570 Planarity : 0.005 0.152 5084 Dihedral : 14.609 90.804 11072 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.63 % Favored : 91.17 % Rotamer: Outliers : 0.16 % Allowed : 0.50 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.14), residues: 3602 helix: -0.18 (0.11), residues: 2316 sheet: -3.36 (0.58), residues: 56 loop : -2.65 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A2196 HIS 0.011 0.001 HIS A3716 PHE 0.044 0.002 PHE A 138 TYR 0.057 0.002 TYR A1802 ARG 0.010 0.001 ARG A1606 Details of bonding type rmsd hydrogen bonds : bond 0.09325 ( 1600) hydrogen bonds : angle 5.26767 ( 4710) covalent geometry : bond 0.00726 (29630) covalent geometry : angle 0.86646 (40078) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 338 time to evaluate : 3.657 Fit side-chains revert: symmetry clash REVERT: A 1348 LEU cc_start: 0.8900 (mt) cc_final: 0.8661 (mt) REVERT: A 1385 ASN cc_start: 0.7085 (t0) cc_final: 0.6840 (t0) REVERT: A 1592 MET cc_start: 0.8351 (tpt) cc_final: 0.8051 (tpp) REVERT: A 1606 ARG cc_start: 0.8494 (mtp-110) cc_final: 0.8262 (mtm110) REVERT: A 1617 LYS cc_start: 0.9271 (mptt) cc_final: 0.9001 (mmmt) REVERT: A 1876 ILE cc_start: 0.9307 (tp) cc_final: 0.8646 (tp) REVERT: A 1880 MET cc_start: 0.7870 (mpp) cc_final: 0.7591 (mpp) REVERT: A 1945 TYR cc_start: 0.8959 (t80) cc_final: 0.8631 (t80) REVERT: A 2220 MET cc_start: 0.8687 (mpp) cc_final: 0.8102 (mpp) REVERT: A 2239 LYS cc_start: 0.8667 (tmtt) cc_final: 0.8434 (tmtt) REVERT: A 2411 LEU cc_start: 0.8252 (tp) cc_final: 0.7855 (tp) REVERT: A 3643 HIS cc_start: 0.7857 (t-170) cc_final: 0.7481 (t-170) outliers start: 5 outliers final: 2 residues processed: 343 average time/residue: 0.4517 time to fit residues: 256.7978 Evaluate side-chains 275 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 273 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 3714 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 306 optimal weight: 0.6980 chunk 275 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 284 optimal weight: 0.0000 chunk 110 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 329 optimal weight: 0.7980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 GLN A1083 ASN A1817 GLN A2270 ASN A2426 HIS ** A2496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2859 GLN A3162 ASN A3664 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.139552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.099255 restraints weight = 60736.331| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.05 r_work: 0.3273 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29630 Z= 0.144 Angle : 0.699 11.069 40078 Z= 0.352 Chirality : 0.043 0.302 4570 Planarity : 0.005 0.093 5084 Dihedral : 6.033 75.553 3945 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.91 % Favored : 93.00 % Rotamer: Outliers : 0.75 % Allowed : 7.61 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.08 (0.14), residues: 3602 helix: 0.19 (0.11), residues: 2337 sheet: -2.62 (0.68), residues: 47 loop : -2.39 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2196 HIS 0.008 0.001 HIS A1304 PHE 0.025 0.002 PHE A1001 TYR 0.024 0.002 TYR A3540 ARG 0.006 0.000 ARG A2530 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 1600) hydrogen bonds : angle 4.53393 ( 4710) covalent geometry : bond 0.00322 (29630) covalent geometry : angle 0.69890 (40078) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 314 time to evaluate : 3.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.2222 (mmt) cc_final: 0.0806 (tmm) REVERT: A 326 MET cc_start: 0.8591 (ppp) cc_final: 0.8367 (ptt) REVERT: A 989 MET cc_start: 0.9247 (mmt) cc_final: 0.8841 (mmt) REVERT: A 1617 LYS cc_start: 0.9298 (mptt) cc_final: 0.8951 (mmmt) REVERT: A 1774 MET cc_start: 0.7692 (tpp) cc_final: 0.7283 (mmm) REVERT: A 1777 LEU cc_start: 0.9171 (mt) cc_final: 0.8655 (mt) REVERT: A 1876 ILE cc_start: 0.9418 (tp) cc_final: 0.8810 (tp) REVERT: A 2128 PHE cc_start: 0.7684 (t80) cc_final: 0.7424 (t80) REVERT: A 2218 PHE cc_start: 0.8496 (t80) cc_final: 0.8107 (t80) REVERT: A 2239 LYS cc_start: 0.8483 (tmtt) cc_final: 0.8275 (tmtt) REVERT: A 2312 TYR cc_start: 0.6101 (m-10) cc_final: 0.5884 (m-10) REVERT: A 2424 MET cc_start: 0.7533 (ptp) cc_final: 0.7193 (ptp) REVERT: A 3168 TYR cc_start: 0.8916 (m-80) cc_final: 0.8714 (m-80) REVERT: A 3414 MET cc_start: 0.9031 (mmm) cc_final: 0.8625 (tpp) REVERT: A 3470 GLN cc_start: 0.7864 (mt0) cc_final: 0.7537 (mt0) REVERT: A 3643 HIS cc_start: 0.8060 (t-170) cc_final: 0.7748 (t-170) REVERT: A 3846 MET cc_start: 0.8625 (tpp) cc_final: 0.8181 (tpp) REVERT: A 4003 ASP cc_start: 0.8369 (t0) cc_final: 0.8149 (t0) outliers start: 24 outliers final: 10 residues processed: 324 average time/residue: 0.4526 time to fit residues: 246.1173 Evaluate side-chains 287 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 277 time to evaluate : 3.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1487 VAL Chi-restraints excluded: chain A residue 2393 LEU Chi-restraints excluded: chain A residue 2399 GLU Chi-restraints excluded: chain A residue 3689 ASP Chi-restraints excluded: chain A residue 4065 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 134 optimal weight: 7.9990 chunk 295 optimal weight: 2.9990 chunk 229 optimal weight: 0.9990 chunk 182 optimal weight: 0.9990 chunk 290 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 360 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 285 optimal weight: 0.6980 chunk 223 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN A 399 GLN A1817 GLN ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2103 HIS A2496 GLN A2784 GLN ** A3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.140332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.100178 restraints weight = 61104.390| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.06 r_work: 0.3292 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29630 Z= 0.132 Angle : 0.656 10.873 40078 Z= 0.328 Chirality : 0.041 0.227 4570 Planarity : 0.004 0.073 5084 Dihedral : 5.565 72.826 3938 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.47 % Favored : 93.48 % Rotamer: Outliers : 1.31 % Allowed : 10.02 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.79 (0.14), residues: 3602 helix: 0.39 (0.11), residues: 2338 sheet: -2.30 (0.70), residues: 47 loop : -2.24 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2164 HIS 0.006 0.001 HIS A1304 PHE 0.022 0.001 PHE A1001 TYR 0.027 0.001 TYR A1086 ARG 0.005 0.000 ARG A2530 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 1600) hydrogen bonds : angle 4.33150 ( 4710) covalent geometry : bond 0.00296 (29630) covalent geometry : angle 0.65596 (40078) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 308 time to evaluate : 6.162 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: A 96 MET cc_start: 0.2182 (mmt) cc_final: 0.0817 (tmm) REVERT: A 300 TRP cc_start: 0.7065 (m100) cc_final: 0.5868 (m100) REVERT: A 326 MET cc_start: 0.8507 (ppp) cc_final: 0.8303 (ptp) REVERT: A 342 MET cc_start: 0.7491 (mmm) cc_final: 0.7148 (mmm) REVERT: A 989 MET cc_start: 0.9255 (mmt) cc_final: 0.8929 (mmt) REVERT: A 1197 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8941 (pp) REVERT: A 1617 LYS cc_start: 0.9297 (mptt) cc_final: 0.8963 (mmmt) REVERT: A 1774 MET cc_start: 0.7695 (tpp) cc_final: 0.7261 (mmm) REVERT: A 1785 ILE cc_start: 0.8290 (mm) cc_final: 0.8061 (mm) REVERT: A 2128 PHE cc_start: 0.7599 (t80) cc_final: 0.7343 (t80) REVERT: A 2196 TRP cc_start: 0.6664 (OUTLIER) cc_final: 0.6221 (m-10) REVERT: A 2218 PHE cc_start: 0.8436 (t80) cc_final: 0.8056 (t80) REVERT: A 2239 LYS cc_start: 0.8413 (tmtt) cc_final: 0.8180 (tmtt) REVERT: A 2312 TYR cc_start: 0.6062 (m-10) cc_final: 0.5829 (m-10) REVERT: A 2351 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8717 (mp10) REVERT: A 2496 GLN cc_start: 0.7279 (OUTLIER) cc_final: 0.6685 (mm-40) REVERT: A 3414 MET cc_start: 0.9087 (mmm) cc_final: 0.8563 (tpp) REVERT: A 3470 GLN cc_start: 0.7778 (mt0) cc_final: 0.7351 (mt0) REVERT: A 3643 HIS cc_start: 0.8075 (t-170) cc_final: 0.7782 (t-170) REVERT: A 4020 MET cc_start: 0.8521 (tpp) cc_final: 0.8234 (tpp) outliers start: 42 outliers final: 20 residues processed: 333 average time/residue: 0.4484 time to fit residues: 250.9743 Evaluate side-chains 303 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 279 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1487 VAL Chi-restraints excluded: chain A residue 1716 GLN Chi-restraints excluded: chain A residue 1792 VAL Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1880 MET Chi-restraints excluded: chain A residue 2196 TRP Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2393 LEU Chi-restraints excluded: chain A residue 2399 GLU Chi-restraints excluded: chain A residue 2496 GLN Chi-restraints excluded: chain A residue 2531 LEU Chi-restraints excluded: chain A residue 3445 LEU Chi-restraints excluded: chain A residue 3689 ASP Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 4065 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 216 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 358 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 221 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 175 optimal weight: 0.9990 chunk 21 optimal weight: 40.0000 chunk 125 optimal weight: 0.5980 chunk 40 optimal weight: 9.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2103 HIS A2152 ASN A2234 ASN A2496 GLN ** A3580 ASN ** 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 = 0.4121 r_free = 0.4121 target = 0.140361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.100868 restraints weight = 61506.456| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.10 r_work: 0.3288 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29630 Z= 0.136 Angle : 0.657 11.640 40078 Z= 0.325 Chirality : 0.042 0.243 4570 Planarity : 0.004 0.065 5084 Dihedral : 5.490 72.484 3938 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.55 % Favored : 93.39 % Rotamer: Outliers : 1.50 % Allowed : 11.71 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.65 (0.14), residues: 3602 helix: 0.49 (0.11), residues: 2342 sheet: -2.19 (0.71), residues: 47 loop : -2.17 (0.18), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A4027 HIS 0.004 0.001 HIS A1304 PHE 0.020 0.001 PHE A1923 TYR 0.020 0.001 TYR A3540 ARG 0.004 0.000 ARG A2530 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 1600) hydrogen bonds : angle 4.26647 ( 4710) covalent geometry : bond 0.00313 (29630) covalent geometry : angle 0.65700 (40078) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 309 time to evaluate : 3.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.2126 (mmt) cc_final: 0.0839 (tmm) REVERT: A 300 TRP cc_start: 0.7058 (m100) cc_final: 0.5859 (m100) REVERT: A 342 MET cc_start: 0.7378 (mmm) cc_final: 0.6929 (mmm) REVERT: A 384 MET cc_start: 0.9014 (ptp) cc_final: 0.8740 (ptp) REVERT: A 857 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8015 (mt0) REVERT: A 989 MET cc_start: 0.9269 (mmt) cc_final: 0.8958 (mmt) REVERT: A 1197 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8938 (pp) REVERT: A 1408 MET cc_start: 0.8771 (tpp) cc_final: 0.8549 (ttt) REVERT: A 1617 LYS cc_start: 0.9251 (mptt) cc_final: 0.8915 (mmmt) REVERT: A 1632 TRP cc_start: 0.7572 (m-10) cc_final: 0.7367 (m-10) REVERT: A 1774 MET cc_start: 0.8160 (tpp) cc_final: 0.7753 (mmm) REVERT: A 2196 TRP cc_start: 0.6653 (OUTLIER) cc_final: 0.6144 (m-10) REVERT: A 2218 PHE cc_start: 0.8426 (t80) cc_final: 0.8058 (t80) REVERT: A 2312 TYR cc_start: 0.6166 (m-10) cc_final: 0.5952 (m-10) REVERT: A 2351 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8699 (mp10) REVERT: A 2359 LYS cc_start: 0.8350 (mmtt) cc_final: 0.7877 (tptt) REVERT: A 2496 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7406 (mm-40) REVERT: A 3414 MET cc_start: 0.9060 (mmm) cc_final: 0.8685 (tpt) REVERT: A 3470 GLN cc_start: 0.7780 (mt0) cc_final: 0.7576 (mt0) REVERT: A 3643 HIS cc_start: 0.8165 (t-170) cc_final: 0.7933 (t-170) REVERT: A 3666 LEU cc_start: 0.8584 (mt) cc_final: 0.8310 (mt) outliers start: 48 outliers final: 22 residues processed: 343 average time/residue: 0.3947 time to fit residues: 227.0428 Evaluate side-chains 307 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 280 time to evaluate : 4.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 857 GLN Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1487 VAL Chi-restraints excluded: chain A residue 1804 MET Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 2196 TRP Chi-restraints excluded: chain A residue 2210 VAL Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2393 LEU Chi-restraints excluded: chain A residue 2399 GLU Chi-restraints excluded: chain A residue 2496 GLN Chi-restraints excluded: chain A residue 2531 LEU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3679 ASN Chi-restraints excluded: chain A residue 3689 ASP Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3810 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 219 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 130 optimal weight: 0.0870 chunk 215 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 340 optimal weight: 0.7980 chunk 297 optimal weight: 0.7980 chunk 305 optimal weight: 3.9990 chunk 331 optimal weight: 1.9990 chunk 348 optimal weight: 0.5980 chunk 181 optimal weight: 5.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1946 ASN A2103 HIS A3580 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.140900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.100746 restraints weight = 61024.223| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.04 r_work: 0.3294 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29630 Z= 0.126 Angle : 0.655 12.419 40078 Z= 0.321 Chirality : 0.041 0.264 4570 Planarity : 0.004 0.061 5084 Dihedral : 5.401 72.548 3938 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.97 % Favored : 93.98 % Rotamer: Outliers : 1.31 % Allowed : 13.24 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3602 helix: 0.59 (0.11), residues: 2337 sheet: -2.10 (0.69), residues: 47 loop : -2.13 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A4027 HIS 0.005 0.001 HIS A1304 PHE 0.026 0.001 PHE A2128 TYR 0.019 0.001 TYR A3540 ARG 0.004 0.000 ARG A2530 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 1600) hydrogen bonds : angle 4.21917 ( 4710) covalent geometry : bond 0.00287 (29630) covalent geometry : angle 0.65479 (40078) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 310 time to evaluate : 3.688 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: A 96 MET cc_start: 0.2136 (mmt) cc_final: 0.0928 (tmm) REVERT: A 300 TRP cc_start: 0.7055 (m100) cc_final: 0.5840 (m100) REVERT: A 342 MET cc_start: 0.7444 (mmm) cc_final: 0.7086 (mmm) REVERT: A 344 GLN cc_start: 0.8824 (mm110) cc_final: 0.8444 (mm110) REVERT: A 857 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7983 (mt0) REVERT: A 989 MET cc_start: 0.9276 (mmt) cc_final: 0.8971 (mmt) REVERT: A 1197 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8974 (pp) REVERT: A 2196 TRP cc_start: 0.6750 (OUTLIER) cc_final: 0.6247 (m-10) REVERT: A 2218 PHE cc_start: 0.8442 (t80) cc_final: 0.8078 (t80) REVERT: A 2312 TYR cc_start: 0.6533 (m-10) cc_final: 0.6267 (m-10) REVERT: A 3643 HIS cc_start: 0.8075 (t-170) cc_final: 0.7862 (t-170) REVERT: A 3666 LEU cc_start: 0.8589 (mt) cc_final: 0.8327 (mt) REVERT: A 3846 MET cc_start: 0.8404 (tpp) cc_final: 0.7982 (tpp) outliers start: 42 outliers final: 26 residues processed: 335 average time/residue: 0.4091 time to fit residues: 228.4463 Evaluate side-chains 310 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 281 time to evaluate : 3.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 857 GLN Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1487 VAL Chi-restraints excluded: chain A residue 1792 VAL Chi-restraints excluded: chain A residue 1804 MET Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 2196 TRP Chi-restraints excluded: chain A residue 2210 VAL Chi-restraints excluded: chain A residue 2223 VAL Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2393 LEU Chi-restraints excluded: chain A residue 2399 GLU Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3679 ASN Chi-restraints excluded: chain A residue 3689 ASP Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3810 VAL Chi-restraints excluded: chain A residue 4065 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 9 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 chunk 272 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 273 optimal weight: 0.5980 chunk 293 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 chunk 335 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1817 GLN A2103 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.140737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.100405 restraints weight = 61219.998| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.08 r_work: 0.3297 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29630 Z= 0.133 Angle : 0.660 11.917 40078 Z= 0.323 Chirality : 0.041 0.312 4570 Planarity : 0.004 0.058 5084 Dihedral : 5.309 72.794 3938 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.39 % Favored : 93.59 % Rotamer: Outliers : 1.56 % Allowed : 14.52 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3602 helix: 0.66 (0.11), residues: 2339 sheet: -1.99 (0.69), residues: 47 loop : -2.08 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A4027 HIS 0.008 0.001 HIS A1304 PHE 0.019 0.001 PHE A2257 TYR 0.025 0.001 TYR A 346 ARG 0.005 0.000 ARG A1606 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 1600) hydrogen bonds : angle 4.18359 ( 4710) covalent geometry : bond 0.00308 (29630) covalent geometry : angle 0.66041 (40078) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 303 time to evaluate : 5.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.2364 (mmt) cc_final: 0.1207 (tmm) REVERT: A 300 TRP cc_start: 0.7058 (m100) cc_final: 0.5844 (m100) REVERT: A 342 MET cc_start: 0.7525 (mmm) cc_final: 0.7089 (mmm) REVERT: A 344 GLN cc_start: 0.8849 (mm110) cc_final: 0.8430 (mm110) REVERT: A 857 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7976 (mt0) REVERT: A 989 MET cc_start: 0.9279 (mmt) cc_final: 0.8979 (mmt) REVERT: A 1197 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8874 (pp) REVERT: A 1408 MET cc_start: 0.8763 (tpp) cc_final: 0.8532 (ttt) REVERT: A 1880 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7133 (mpp) REVERT: A 1975 LEU cc_start: 0.4175 (OUTLIER) cc_final: 0.3892 (pt) REVERT: A 2196 TRP cc_start: 0.6865 (OUTLIER) cc_final: 0.6304 (m-10) REVERT: A 2218 PHE cc_start: 0.8378 (t80) cc_final: 0.8029 (t80) REVERT: A 2312 TYR cc_start: 0.6567 (m-10) cc_final: 0.6346 (m-10) REVERT: A 2377 ARG cc_start: 0.8548 (mpt-90) cc_final: 0.8291 (mpt-90) REVERT: A 2399 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8576 (pm20) REVERT: A 3643 HIS cc_start: 0.8075 (t-170) cc_final: 0.7865 (t-170) REVERT: A 3846 MET cc_start: 0.8535 (tpp) cc_final: 0.8121 (tpp) outliers start: 50 outliers final: 29 residues processed: 334 average time/residue: 0.6222 time to fit residues: 352.3187 Evaluate side-chains 321 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 286 time to evaluate : 6.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 857 GLN Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1487 VAL Chi-restraints excluded: chain A residue 1724 MET Chi-restraints excluded: chain A residue 1792 VAL Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1880 MET Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2196 TRP Chi-restraints excluded: chain A residue 2210 VAL Chi-restraints excluded: chain A residue 2223 VAL Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2393 LEU Chi-restraints excluded: chain A residue 2399 GLU Chi-restraints excluded: chain A residue 2531 LEU Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3679 ASN Chi-restraints excluded: chain A residue 3689 ASP Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3810 VAL Chi-restraints excluded: chain A residue 4031 ILE Chi-restraints excluded: chain A residue 4065 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 95 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 319 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 325 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 257 optimal weight: 10.0000 chunk 178 optimal weight: 0.8980 chunk 203 optimal weight: 20.0000 chunk 245 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2103 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.141247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.101355 restraints weight = 61001.168| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.10 r_work: 0.3311 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29630 Z= 0.125 Angle : 0.659 12.441 40078 Z= 0.321 Chirality : 0.041 0.304 4570 Planarity : 0.004 0.055 5084 Dihedral : 5.237 72.318 3938 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.89 % Favored : 94.09 % Rotamer: Outliers : 1.47 % Allowed : 14.99 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3602 helix: 0.70 (0.11), residues: 2342 sheet: -1.88 (0.69), residues: 49 loop : -2.04 (0.18), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A4027 HIS 0.006 0.001 HIS A1304 PHE 0.021 0.001 PHE A2145 TYR 0.018 0.001 TYR A3540 ARG 0.003 0.000 ARG A1606 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 1600) hydrogen bonds : angle 4.18034 ( 4710) covalent geometry : bond 0.00285 (29630) covalent geometry : angle 0.65915 (40078) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 305 time to evaluate : 6.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.2320 (mmt) cc_final: 0.1192 (tmm) REVERT: A 300 TRP cc_start: 0.7013 (m100) cc_final: 0.5922 (m100) REVERT: A 326 MET cc_start: 0.8600 (ppp) cc_final: 0.8264 (ptt) REVERT: A 340 TYR cc_start: 0.8481 (t80) cc_final: 0.8015 (t80) REVERT: A 342 MET cc_start: 0.7488 (mmm) cc_final: 0.7264 (mmm) REVERT: A 344 GLN cc_start: 0.8933 (mm110) cc_final: 0.8538 (mm-40) REVERT: A 346 TYR cc_start: 0.8552 (m-80) cc_final: 0.8309 (m-80) REVERT: A 453 MET cc_start: 0.7549 (tpp) cc_final: 0.7200 (tpp) REVERT: A 857 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7944 (mt0) REVERT: A 989 MET cc_start: 0.9275 (mmt) cc_final: 0.8969 (mmt) REVERT: A 1197 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8868 (pp) REVERT: A 1592 MET cc_start: 0.8678 (tpt) cc_final: 0.8438 (tpp) REVERT: A 1785 ILE cc_start: 0.8262 (mm) cc_final: 0.8005 (mm) REVERT: A 1871 MET cc_start: 0.8944 (ppp) cc_final: 0.8363 (ppp) REVERT: A 1880 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7114 (mpp) REVERT: A 1938 ARG cc_start: 0.8668 (tmm160) cc_final: 0.8464 (ptm-80) REVERT: A 2196 TRP cc_start: 0.6717 (OUTLIER) cc_final: 0.6253 (m-10) REVERT: A 2218 PHE cc_start: 0.8378 (t80) cc_final: 0.8041 (t80) REVERT: A 2359 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8001 (tptt) REVERT: A 2377 ARG cc_start: 0.8576 (mpt-90) cc_final: 0.8323 (mpt-90) REVERT: A 2399 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8637 (pm20) REVERT: A 2565 MET cc_start: 0.8820 (mmp) cc_final: 0.8457 (mmm) REVERT: A 3846 MET cc_start: 0.8535 (tpp) cc_final: 0.8078 (tpp) REVERT: A 3959 MET cc_start: 0.9102 (pmm) cc_final: 0.8570 (pmm) outliers start: 47 outliers final: 32 residues processed: 335 average time/residue: 0.5490 time to fit residues: 314.6247 Evaluate side-chains 320 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 283 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 857 GLN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1487 VAL Chi-restraints excluded: chain A residue 1716 GLN Chi-restraints excluded: chain A residue 1792 VAL Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1880 MET Chi-restraints excluded: chain A residue 2088 LEU Chi-restraints excluded: chain A residue 2196 TRP Chi-restraints excluded: chain A residue 2210 VAL Chi-restraints excluded: chain A residue 2223 VAL Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2393 LEU Chi-restraints excluded: chain A residue 2399 GLU Chi-restraints excluded: chain A residue 2531 LEU Chi-restraints excluded: chain A residue 2944 THR Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3679 ASN Chi-restraints excluded: chain A residue 3689 ASP Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3810 VAL Chi-restraints excluded: chain A residue 4031 ILE Chi-restraints excluded: chain A residue 4065 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 274 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 104 optimal weight: 0.7980 chunk 269 optimal weight: 0.7980 chunk 167 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 299 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2103 HIS A2426 HIS A3643 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.141187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.101243 restraints weight = 61240.563| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.10 r_work: 0.3303 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29630 Z= 0.132 Angle : 0.672 12.398 40078 Z= 0.325 Chirality : 0.041 0.321 4570 Planarity : 0.004 0.055 5084 Dihedral : 5.198 72.274 3938 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.47 % Allowed : 15.49 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3602 helix: 0.71 (0.11), residues: 2339 sheet: -1.43 (0.75), residues: 43 loop : -2.00 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A4027 HIS 0.010 0.001 HIS A3643 PHE 0.019 0.001 PHE A1923 TYR 0.019 0.001 TYR A3540 ARG 0.008 0.000 ARG A1936 Details of bonding type rmsd hydrogen bonds : bond 0.03337 ( 1600) hydrogen bonds : angle 4.17835 ( 4710) covalent geometry : bond 0.00306 (29630) covalent geometry : angle 0.67159 (40078) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 303 time to evaluate : 3.333 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: A 96 MET cc_start: 0.2314 (mmt) cc_final: 0.1183 (tmm) REVERT: A 208 MET cc_start: 0.4593 (ptt) cc_final: 0.3931 (mmt) REVERT: A 300 TRP cc_start: 0.7030 (m100) cc_final: 0.5940 (m100) REVERT: A 326 MET cc_start: 0.8527 (ppp) cc_final: 0.8286 (ptt) REVERT: A 340 TYR cc_start: 0.8491 (t80) cc_final: 0.8040 (t80) REVERT: A 342 MET cc_start: 0.7576 (mmm) cc_final: 0.7236 (mmm) REVERT: A 344 GLN cc_start: 0.8920 (mm110) cc_final: 0.8523 (mm-40) REVERT: A 453 MET cc_start: 0.7556 (tpp) cc_final: 0.7198 (tpp) REVERT: A 857 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7975 (mt0) REVERT: A 989 MET cc_start: 0.9281 (mmt) cc_final: 0.8981 (mmt) REVERT: A 1119 LYS cc_start: 0.8407 (mmtt) cc_final: 0.8171 (mmtt) REVERT: A 1197 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8878 (pp) REVERT: A 1408 MET cc_start: 0.8705 (tpp) cc_final: 0.8493 (ttt) REVERT: A 1592 MET cc_start: 0.8666 (tpt) cc_final: 0.8413 (tpp) REVERT: A 1617 LYS cc_start: 0.9357 (mptt) cc_final: 0.9024 (mmmt) REVERT: A 1880 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7121 (mpp) REVERT: A 2196 TRP cc_start: 0.6697 (OUTLIER) cc_final: 0.6231 (m-10) REVERT: A 2218 PHE cc_start: 0.8404 (t80) cc_final: 0.8076 (t80) REVERT: A 2377 ARG cc_start: 0.8582 (mpt-90) cc_final: 0.8289 (mpt-90) REVERT: A 2399 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8651 (pm20) REVERT: A 3846 MET cc_start: 0.8562 (tpp) cc_final: 0.8106 (tpp) REVERT: A 3959 MET cc_start: 0.9157 (pmm) cc_final: 0.8627 (pmm) outliers start: 47 outliers final: 34 residues processed: 329 average time/residue: 0.4231 time to fit residues: 233.6494 Evaluate side-chains 329 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 290 time to evaluate : 4.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 857 GLN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1086 TYR Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1279 LEU Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1477 HIS Chi-restraints excluded: chain A residue 1487 VAL Chi-restraints excluded: chain A residue 1716 GLN Chi-restraints excluded: chain A residue 1724 MET Chi-restraints excluded: chain A residue 1792 VAL Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1880 MET Chi-restraints excluded: chain A residue 2196 TRP Chi-restraints excluded: chain A residue 2210 VAL Chi-restraints excluded: chain A residue 2223 VAL Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2393 LEU Chi-restraints excluded: chain A residue 2399 GLU Chi-restraints excluded: chain A residue 2531 LEU Chi-restraints excluded: chain A residue 2944 THR Chi-restraints excluded: chain A residue 3454 LEU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3679 ASN Chi-restraints excluded: chain A residue 3689 ASP Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3810 VAL Chi-restraints excluded: chain A residue 4031 ILE Chi-restraints excluded: chain A residue 4065 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 59.1492 > 50: distance: 14 - 41: 9.368 distance: 18 - 51: 21.485 distance: 23 - 59: 31.122 distance: 36 - 41: 6.569 distance: 37 - 67: 13.955 distance: 41 - 42: 7.201 distance: 42 - 43: 10.998 distance: 42 - 45: 7.802 distance: 43 - 44: 15.080 distance: 43 - 51: 15.451 distance: 45 - 46: 7.993 distance: 46 - 47: 9.876 distance: 46 - 48: 9.242 distance: 47 - 49: 6.068 distance: 48 - 50: 3.247 distance: 49 - 50: 5.256 distance: 51 - 52: 25.483 distance: 52 - 53: 32.479 distance: 52 - 55: 9.110 distance: 53 - 54: 20.952 distance: 53 - 59: 20.128 distance: 55 - 56: 16.918 distance: 56 - 57: 12.174 distance: 56 - 58: 18.686 distance: 59 - 60: 3.170 distance: 60 - 61: 20.687 distance: 60 - 63: 31.400 distance: 61 - 62: 12.584 distance: 61 - 67: 25.745 distance: 63 - 64: 6.812 distance: 64 - 65: 25.371 distance: 64 - 66: 29.921 distance: 67 - 68: 7.839 distance: 68 - 69: 4.757 distance: 68 - 71: 12.265 distance: 69 - 70: 8.751 distance: 69 - 79: 20.068 distance: 71 - 72: 10.939 distance: 72 - 73: 9.942 distance: 72 - 74: 4.629 distance: 73 - 75: 13.055 distance: 74 - 76: 4.690 distance: 75 - 77: 3.457 distance: 77 - 78: 9.791 distance: 79 - 80: 9.868 distance: 80 - 81: 15.127 distance: 80 - 83: 9.042 distance: 81 - 82: 14.766 distance: 81 - 90: 25.024 distance: 83 - 84: 13.359 distance: 84 - 85: 9.382 distance: 85 - 86: 9.265 distance: 86 - 87: 5.789 distance: 87 - 88: 19.436 distance: 87 - 89: 30.318 distance: 90 - 91: 14.774 distance: 91 - 92: 16.633 distance: 91 - 94: 12.909 distance: 92 - 93: 12.841 distance: 92 - 98: 27.524 distance: 95 - 96: 5.393 distance: 95 - 97: 15.400 distance: 98 - 99: 8.663 distance: 98 - 104: 12.110 distance: 99 - 100: 10.342 distance: 99 - 102: 41.440 distance: 100 - 101: 35.784 distance: 100 - 105: 18.602 distance: 102 - 103: 11.087 distance: 103 - 104: 41.438 distance: 105 - 106: 9.290 distance: 106 - 107: 13.183 distance: 106 - 109: 17.198 distance: 107 - 108: 15.558 distance: 107 - 114: 5.913 distance: 109 - 110: 15.768 distance: 110 - 111: 25.568 distance: 111 - 112: 14.484 distance: 111 - 113: 15.841 distance: 114 - 115: 6.115 distance: 115 - 116: 11.268 distance: 115 - 118: 8.179 distance: 116 - 117: 18.207 distance: 116 - 120: 11.451 distance: 118 - 119: 12.763 distance: 120 - 121: 4.172 distance: 121 - 122: 6.490 distance: 121 - 124: 9.925 distance: 122 - 123: 11.535 distance: 124 - 125: 6.346 distance: 125 - 126: 6.430 distance: 126 - 127: 4.131 distance: 126 - 128: 4.971