Starting phenix.real_space_refine on Wed Jun 11 21:37:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iz7_61024/06_2025/9iz7_61024.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iz7_61024/06_2025/9iz7_61024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iz7_61024/06_2025/9iz7_61024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iz7_61024/06_2025/9iz7_61024.map" model { file = "/net/cci-nas-00/data/ceres_data/9iz7_61024/06_2025/9iz7_61024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iz7_61024/06_2025/9iz7_61024.cif" } resolution = 4.32 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= 0.005 sd= 0.090 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: 3 Type Number sf(0) Gaussians C 7773 2.51 5 N 2611 2.21 5 O 2612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12996 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 12996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2611, 12996 Classifications: {'peptide': 2611} Incomplete info: {'truncation_to_alanine': 2427} Link IDs: {'PTRANS': 77, 'TRANS': 2533} Chain breaks: 17 Unresolved chain link angles: 77 Unresolved non-hydrogen bonds: 8944 Unresolved non-hydrogen angles: 11452 Unresolved non-hydrogen dihedrals: 7596 Unresolved non-hydrogen chiralities: 785 Planarities with less than four sites: {'GLN:plan1': 98, 'HIS:plan': 62, 'TYR:plan': 121, 'ASN:plan1': 143, 'TRP:plan': 34, 'ASP:plan': 131, 'PHE:plan': 179, 'GLU:plan': 155, 'ARG:plan': 104} Unresolved non-hydrogen planarities: 4891 Time building chain proxies: 9.03, per 1000 atoms: 0.69 Number of scatterers: 12996 At special positions: 0 Unit cell: (146.26, 93.72, 207.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2612 8.00 N 2611 7.00 C 7773 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: 4.31 Conformation dependent library (CDL) restraints added in 2.8 seconds 5146 Ramachandran restraints generated. 2573 Oldfield, 0 Emsley, 2573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5090 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 2 sheets defined 68.2% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 15 through 37 removed outlier: 3.817A pdb=" N SER A 20 " --> pdb=" O ILE A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 68 removed outlier: 3.691A pdb=" N LYS A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 96 Processing helix chain 'A' and resid 98 through 113 removed outlier: 3.785A pdb=" N THR A 113 " --> pdb=" O ILE A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 135 removed outlier: 4.205A pdb=" N PHE A 128 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N SER A 129 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 144 Processing helix chain 'A' and resid 146 through 164 removed outlier: 3.533A pdb=" N GLU A 162 " --> pdb=" O CYS A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.956A pdb=" N GLU A 205 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.656A pdb=" N ALA A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 261 Processing helix chain 'A' and resid 264 through 285 removed outlier: 3.514A pdb=" N ILE A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 311 removed outlier: 4.180A pdb=" N GLN A 293 " --> pdb=" O ASP A 289 " (cutoff:3.500A) Proline residue: A 303 - end of helix removed outlier: 4.242A pdb=" N THR A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TRP A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 332 removed outlier: 3.623A pdb=" N PHE A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 397 removed outlier: 4.552A pdb=" N TYR A 384 " --> pdb=" O PHE A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 430 through 447 removed outlier: 3.892A pdb=" N PHE A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR A 445 " --> pdb=" O MET A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.829A pdb=" N GLN A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 486 removed outlier: 3.692A pdb=" N GLN A 474 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER A 475 " --> pdb=" O ASN A 471 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE A 478 " --> pdb=" O GLN A 474 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N PHE A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 512 removed outlier: 4.266A pdb=" N LYS A 500 " --> pdb=" O THR A 496 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 511 " --> pdb=" O SER A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 522 removed outlier: 4.627A pdb=" N CYS A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 536 through 541 removed outlier: 3.903A pdb=" N PHE A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 577 through 591 Processing helix chain 'A' and resid 612 through 623 removed outlier: 3.627A pdb=" N PHE A 616 " --> pdb=" O SER A 612 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 619 " --> pdb=" O ILE A 615 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N MET A 620 " --> pdb=" O PHE A 616 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N MET A 621 " --> pdb=" O ASP A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 656 removed outlier: 3.594A pdb=" N TRP A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER A 652 " --> pdb=" O LYS A 648 " (cutoff:3.500A) Proline residue: A 653 - end of helix removed outlier: 4.156A pdb=" N LEU A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 647 through 656' Processing helix chain 'A' and resid 683 through 696 removed outlier: 3.639A pdb=" N MET A 693 " --> pdb=" O ASN A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 722 Proline residue: A 716 - end of helix Processing helix chain 'A' and resid 757 through 770 Processing helix chain 'A' and resid 774 through 793 Proline residue: A 790 - end of helix Processing helix chain 'A' and resid 804 through 808 Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.684A pdb=" N LYS A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 901 Processing helix chain 'A' and resid 902 through 907 Processing helix chain 'A' and resid 909 through 919 removed outlier: 3.713A pdb=" N TYR A 916 " --> pdb=" O ALA A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 940 removed outlier: 3.785A pdb=" N PHE A 928 " --> pdb=" O SER A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 948 Processing helix chain 'A' and resid 948 through 962 removed outlier: 3.635A pdb=" N GLN A 960 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 961 " --> pdb=" O LYS A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 985 removed outlier: 4.740A pdb=" N PHE A 983 " --> pdb=" O LYS A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 991 Processing helix chain 'A' and resid 996 through 1009 removed outlier: 4.003A pdb=" N GLN A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR A1001 " --> pdb=" O SER A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1031 Processing helix chain 'A' and resid 1033 through 1048 removed outlier: 4.232A pdb=" N VAL A1045 " --> pdb=" O VAL A1041 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A1048 " --> pdb=" O LEU A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1064 Proline residue: A1062 - end of helix Processing helix chain 'A' and resid 1068 through 1072 removed outlier: 3.762A pdb=" N SER A1071 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A1072 " --> pdb=" O GLU A1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1068 through 1072' Processing helix chain 'A' and resid 1074 through 1088 Processing helix chain 'A' and resid 1092 through 1104 removed outlier: 3.973A pdb=" N ALA A1104 " --> pdb=" O LEU A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1117 removed outlier: 6.258A pdb=" N GLU A1114 " --> pdb=" O SER A1110 " (cutoff:3.500A) Proline residue: A1115 - end of helix Processing helix chain 'A' and resid 1122 through 1128 removed outlier: 4.455A pdb=" N ASN A1126 " --> pdb=" O ILE A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1137 Processing helix chain 'A' and resid 1158 through 1163 Processing helix chain 'A' and resid 1166 through 1182 removed outlier: 4.521A pdb=" N LYS A1171 " --> pdb=" O SER A1167 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE A1178 " --> pdb=" O SER A1174 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LEU A1179 " --> pdb=" O ASP A1175 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A1182 " --> pdb=" O ILE A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1191 Processing helix chain 'A' and resid 1192 through 1198 removed outlier: 3.796A pdb=" N ARG A1196 " --> pdb=" O LEU A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1207 Processing helix chain 'A' and resid 1208 through 1220 removed outlier: 3.901A pdb=" N LEU A1218 " --> pdb=" O THR A1214 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A1219 " --> pdb=" O TYR A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1255 removed outlier: 4.344A pdb=" N GLU A1240 " --> pdb=" O ALA A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1270 through 1283 removed outlier: 4.280A pdb=" N ALA A1283 " --> pdb=" O LEU A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1312 removed outlier: 3.721A pdb=" N VAL A1302 " --> pdb=" O SER A1298 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG A1308 " --> pdb=" O TRP A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1316 Processing helix chain 'A' and resid 1319 through 1334 removed outlier: 3.842A pdb=" N ILE A1323 " --> pdb=" O ILE A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1356 Processing helix chain 'A' and resid 1358 through 1362 Processing helix chain 'A' and resid 1363 through 1378 removed outlier: 3.628A pdb=" N ARG A1375 " --> pdb=" O LEU A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1399 removed outlier: 4.327A pdb=" N LYS A1396 " --> pdb=" O ARG A1392 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS A1397 " --> pdb=" O PHE A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1412 Processing helix chain 'A' and resid 1428 through 1444 removed outlier: 3.692A pdb=" N GLN A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1465 Processing helix chain 'A' and resid 1469 through 1484 removed outlier: 3.973A pdb=" N PHE A1481 " --> pdb=" O SER A1477 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY A1484 " --> pdb=" O LEU A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1492 Processing helix chain 'A' and resid 1492 through 1500 removed outlier: 3.974A pdb=" N CYS A1497 " --> pdb=" O ASN A1493 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A1498 " --> pdb=" O ASN A1494 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1515 removed outlier: 3.650A pdb=" N LEU A1515 " --> pdb=" O VAL A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1517 through 1522 Processing helix chain 'A' and resid 1532 through 1548 removed outlier: 4.264A pdb=" N GLY A1544 " --> pdb=" O SER A1540 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP A1545 " --> pdb=" O ASP A1541 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASN A1546 " --> pdb=" O ILE A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1592 removed outlier: 4.352A pdb=" N ILE A1579 " --> pdb=" O GLU A1575 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE A1580 " --> pdb=" O SER A1576 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TRP A1581 " --> pdb=" O LYS A1577 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A1582 " --> pdb=" O LEU A1578 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS A1589 " --> pdb=" O CYS A1585 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER A1590 " --> pdb=" O GLN A1586 " (cutoff:3.500A) Processing helix chain 'A' and resid 1600 through 1610 removed outlier: 3.529A pdb=" N ASP A1605 " --> pdb=" O SER A1601 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N CYS A1606 " --> pdb=" O PHE A1602 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE A1607 " --> pdb=" O ILE A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1634 removed outlier: 3.848A pdb=" N ASP A1633 " --> pdb=" O SER A1629 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER A1634 " --> pdb=" O ILE A1630 " (cutoff:3.500A) Processing helix chain 'A' and resid 1661 through 1674 Processing helix chain 'A' and resid 1677 through 1690 removed outlier: 3.684A pdb=" N SER A1682 " --> pdb=" O SER A1678 " (cutoff:3.500A) Processing helix chain 'A' and resid 1692 through 1701 Processing helix chain 'A' and resid 1702 through 1710 removed outlier: 4.148A pdb=" N LEU A1706 " --> pdb=" O ILE A1702 " (cutoff:3.500A) Processing helix chain 'A' and resid 1717 through 1731 removed outlier: 4.589A pdb=" N TYR A1721 " --> pdb=" O LYS A1717 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A1731 " --> pdb=" O LEU A1727 " (cutoff:3.500A) Processing helix chain 'A' and resid 1735 through 1748 Processing helix chain 'A' and resid 1759 through 1767 removed outlier: 4.084A pdb=" N VAL A1767 " --> pdb=" O ALA A1763 " (cutoff:3.500A) Processing helix chain 'A' and resid 1770 through 1782 removed outlier: 4.127A pdb=" N HIS A1782 " --> pdb=" O ALA A1778 " (cutoff:3.500A) Processing helix chain 'A' and resid 1786 through 1798 removed outlier: 3.896A pdb=" N PHE A1790 " --> pdb=" O GLN A1786 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A1792 " --> pdb=" O LEU A1788 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1812 removed outlier: 3.969A pdb=" N LEU A1806 " --> pdb=" O ASP A1802 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A1807 " --> pdb=" O ILE A1803 " (cutoff:3.500A) Processing helix chain 'A' and resid 1827 through 1838 removed outlier: 4.186A pdb=" N GLU A1838 " --> pdb=" O LYS A1834 " (cutoff:3.500A) Processing helix chain 'A' and resid 1860 through 1873 Processing helix chain 'A' and resid 1877 through 1888 removed outlier: 3.870A pdb=" N ASP A1884 " --> pdb=" O GLU A1880 " (cutoff:3.500A) Processing helix chain 'A' and resid 1896 through 1906 Processing helix chain 'A' and resid 1921 through 1939 Processing helix chain 'A' and resid 1941 through 1955 removed outlier: 4.040A pdb=" N LEU A1955 " --> pdb=" O LYS A1951 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1969 removed outlier: 4.175A pdb=" N ALA A1969 " --> pdb=" O LEU A1965 " (cutoff:3.500A) Processing helix chain 'A' and resid 1969 through 1980 removed outlier: 4.233A pdb=" N PHE A1976 " --> pdb=" O TYR A1972 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N CYS A1980 " --> pdb=" O PHE A1976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1988 through 1997 removed outlier: 4.178A pdb=" N LEU A1992 " --> pdb=" O ASP A1988 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS A1997 " --> pdb=" O LEU A1993 " (cutoff:3.500A) Processing helix chain 'A' and resid 2013 through 2024 removed outlier: 3.977A pdb=" N LEU A2020 " --> pdb=" O VAL A2016 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU A2021 " --> pdb=" O LEU A2017 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A2022 " --> pdb=" O LEU A2018 " (cutoff:3.500A) Processing helix chain 'A' and resid 2031 through 2037 removed outlier: 3.841A pdb=" N ARG A2037 " --> pdb=" O LEU A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2040 through 2049 removed outlier: 4.451A pdb=" N ILE A2047 " --> pdb=" O GLU A2043 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2072 removed outlier: 4.210A pdb=" N PHE A2061 " --> pdb=" O LEU A2057 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A2065 " --> pdb=" O PHE A2061 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A2066 " --> pdb=" O SER A2062 " (cutoff:3.500A) Processing helix chain 'A' and resid 2080 through 2096 Processing helix chain 'A' and resid 2098 through 2112 removed outlier: 4.065A pdb=" N ILE A2103 " --> pdb=" O LYS A2099 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A2112 " --> pdb=" O GLU A2108 " (cutoff:3.500A) Processing helix chain 'A' and resid 2116 through 2134 removed outlier: 4.099A pdb=" N SER A2120 " --> pdb=" O SER A2116 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A2125 " --> pdb=" O ILE A2121 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A2126 " --> pdb=" O SER A2122 " (cutoff:3.500A) Processing helix chain 'A' and resid 2137 through 2152 removed outlier: 3.905A pdb=" N VAL A2141 " --> pdb=" O LYS A2137 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A2148 " --> pdb=" O ASN A2144 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS A2152 " --> pdb=" O LYS A2148 " (cutoff:3.500A) Processing helix chain 'A' and resid 2159 through 2177 removed outlier: 3.940A pdb=" N LYS A2163 " --> pdb=" O LYS A2159 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A2168 " --> pdb=" O ILE A2164 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE A2171 " --> pdb=" O MET A2167 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS A2172 " --> pdb=" O PHE A2168 " (cutoff:3.500A) Processing helix chain 'A' and resid 2178 through 2204 removed outlier: 4.158A pdb=" N ARG A2204 " --> pdb=" O GLN A2200 " (cutoff:3.500A) Processing helix chain 'A' and resid 2219 through 2261 removed outlier: 4.095A pdb=" N SER A2223 " --> pdb=" O LYS A2219 " (cutoff:3.500A) Processing helix chain 'A' and resid 2264 through 2281 removed outlier: 3.505A pdb=" N ILE A2268 " --> pdb=" O ASN A2264 " (cutoff:3.500A) Processing helix chain 'A' and resid 2283 through 2295 removed outlier: 4.609A pdb=" N SER A2287 " --> pdb=" O GLU A2283 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N HIS A2290 " --> pdb=" O ASN A2286 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N TYR A2291 " --> pdb=" O SER A2287 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A2293 " --> pdb=" O GLN A2289 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN A2294 " --> pdb=" O HIS A2290 " (cutoff:3.500A) Processing helix chain 'A' and resid 2296 through 2300 removed outlier: 3.948A pdb=" N LYS A2299 " --> pdb=" O PRO A2296 " (cutoff:3.500A) Processing helix chain 'A' and resid 2303 through 2311 Processing helix chain 'A' and resid 2316 through 2333 Processing helix chain 'A' and resid 2333 through 2347 removed outlier: 4.291A pdb=" N SER A2337 " --> pdb=" O HIS A2333 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N HIS A2339 " --> pdb=" O TYR A2335 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL A2340 " --> pdb=" O HIS A2336 " (cutoff:3.500A) Processing helix chain 'A' and resid 2354 through 2371 removed outlier: 3.527A pdb=" N SER A2358 " --> pdb=" O LEU A2354 " (cutoff:3.500A) Processing helix chain 'A' and resid 2373 through 2396 Processing helix chain 'A' and resid 2414 through 2423 removed outlier: 3.715A pdb=" N ASN A2422 " --> pdb=" O LYS A2418 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A2423 " --> pdb=" O ASP A2419 " (cutoff:3.500A) Processing helix chain 'A' and resid 2486 through 2506 Processing helix chain 'A' and resid 2546 through 2552 removed outlier: 3.700A pdb=" N VAL A2550 " --> pdb=" O SER A2546 " (cutoff:3.500A) Processing helix chain 'A' and resid 2557 through 2568 removed outlier: 4.057A pdb=" N LYS A2568 " --> pdb=" O LEU A2564 " (cutoff:3.500A) Processing helix chain 'A' and resid 2572 through 2587 removed outlier: 3.753A pdb=" N LEU A2577 " --> pdb=" O LEU A2573 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG A2585 " --> pdb=" O ASP A2581 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS A2586 " --> pdb=" O LEU A2582 " (cutoff:3.500A) Processing helix chain 'A' and resid 2592 through 2596 Processing helix chain 'A' and resid 2603 through 2627 removed outlier: 4.185A pdb=" N THR A2610 " --> pdb=" O PHE A2606 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A2611 " --> pdb=" O THR A2607 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A2620 " --> pdb=" O THR A2616 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL A2625 " --> pdb=" O VAL A2621 " (cutoff:3.500A) Processing helix chain 'A' and resid 2656 through 2660 Processing helix chain 'A' and resid 2671 through 2677 Processing helix chain 'A' and resid 2685 through 2695 removed outlier: 3.824A pdb=" N LEU A2695 " --> pdb=" O MET A2691 " (cutoff:3.500A) Processing helix chain 'A' and resid 2695 through 2701 removed outlier: 4.380A pdb=" N ARG A2699 " --> pdb=" O LEU A2695 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A2700 " --> pdb=" O GLU A2696 " (cutoff:3.500A) Processing helix chain 'A' and resid 2701 through 2714 removed outlier: 4.603A pdb=" N LEU A2705 " --> pdb=" O GLU A2701 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU A2706 " --> pdb=" O GLU A2702 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A2712 " --> pdb=" O VAL A2708 " (cutoff:3.500A) Processing helix chain 'A' and resid 2723 through 2730 removed outlier: 3.770A pdb=" N MET A2728 " --> pdb=" O PRO A2724 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS A2729 " --> pdb=" O LEU A2725 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS A2730 " --> pdb=" O ARG A2726 " (cutoff:3.500A) Processing helix chain 'A' and resid 2744 through 2751 Processing helix chain 'A' and resid 2765 through 2778 Processing helix chain 'A' and resid 2783 through 2796 removed outlier: 3.955A pdb=" N VAL A2788 " --> pdb=" O VAL A2784 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A2789 " --> pdb=" O GLU A2785 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE A2794 " --> pdb=" O GLU A2790 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN A2796 " --> pdb=" O ILE A2792 " (cutoff:3.500A) Processing helix chain 'A' and resid 2797 through 2803 removed outlier: 4.149A pdb=" N LEU A2801 " --> pdb=" O ASP A2797 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A2802 " --> pdb=" O PRO A2798 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU A2803 " --> pdb=" O SER A2799 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2797 through 2803' Processing sheet with id=AA1, first strand: chain 'A' and resid 2464 through 2465 Processing sheet with id=AA2, first strand: chain 'A' and resid 2538 through 2539 removed outlier: 3.535A pdb=" N ILE A2638 " --> pdb=" O ILE A2538 " (cutoff:3.500A) 1071 hydrogen bonds defined for protein. 3165 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.18 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.54: 12962 1.54 - 1.89: 16 1.89 - 2.25: 0 2.25 - 2.60: 0 2.60 - 2.95: 1 Bond restraints: 12979 Sorted by residual: bond pdb=" C PRO A2716 " pdb=" N PHE A2718 " ideal model delta sigma weight residual 1.330 2.954 -1.624 1.38e-02 5.25e+03 1.39e+04 bond pdb=" C GLY A2744 " pdb=" O GLY A2744 " ideal model delta sigma weight residual 1.230 1.334 -0.104 1.38e-02 5.25e+03 5.65e+01 bond pdb=" CA THR A2748 " pdb=" CB THR A2748 " ideal model delta sigma weight residual 1.527 1.634 -0.107 1.61e-02 3.86e+03 4.40e+01 bond pdb=" C THR A2747 " pdb=" O THR A2747 " ideal model delta sigma weight residual 1.232 1.315 -0.082 1.37e-02 5.33e+03 3.60e+01 bond pdb=" CA ASN A2745 " pdb=" C ASN A2745 " ideal model delta sigma weight residual 1.528 1.460 0.067 1.36e-02 5.41e+03 2.45e+01 ... (remaining 12974 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.42: 18095 10.42 - 20.85: 4 20.85 - 31.27: 0 31.27 - 41.69: 1 41.69 - 52.11: 1 Bond angle restraints: 18101 Sorted by residual: angle pdb=" O PRO A2716 " pdb=" C PRO A2716 " pdb=" N PHE A2718 " ideal model delta sigma weight residual 122.64 70.53 52.11 1.35e+00 5.49e-01 1.49e+03 angle pdb=" CA PRO A2716 " pdb=" C PRO A2716 " pdb=" N PHE A2718 " ideal model delta sigma weight residual 116.70 84.04 32.66 2.07e+00 2.33e-01 2.49e+02 angle pdb=" N GLY A2744 " pdb=" CA GLY A2744 " pdb=" C GLY A2744 " ideal model delta sigma weight residual 112.37 124.24 -11.87 1.40e+00 5.10e-01 7.19e+01 angle pdb=" N LYS A2730 " pdb=" CA LYS A2730 " pdb=" C LYS A2730 " ideal model delta sigma weight residual 110.80 128.04 -17.24 2.13e+00 2.20e-01 6.55e+01 angle pdb=" N ASN A2745 " pdb=" CA ASN A2745 " pdb=" C ASN A2745 " ideal model delta sigma weight residual 111.17 100.27 10.90 1.41e+00 5.03e-01 5.97e+01 ... (remaining 18096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.57: 7331 9.57 - 19.14: 313 19.14 - 28.70: 37 28.70 - 38.27: 3 38.27 - 47.84: 2 Dihedral angle restraints: 7686 sinusoidal: 3 harmonic: 7683 Sorted by residual: dihedral pdb=" CA SER A2000 " pdb=" C SER A2000 " pdb=" N SER A2001 " pdb=" CA SER A2001 " ideal model delta harmonic sigma weight residual -180.00 -132.16 -47.84 0 5.00e+00 4.00e-02 9.15e+01 dihedral pdb=" CA PRO A2716 " pdb=" C PRO A2716 " pdb=" N PHE A2718 " pdb=" CA PHE A2718 " ideal model delta harmonic sigma weight residual 180.00 139.84 40.16 0 5.00e+00 4.00e-02 6.45e+01 dihedral pdb=" CA HIS A 138 " pdb=" C HIS A 138 " pdb=" N SER A 139 " pdb=" CA SER A 139 " ideal model delta harmonic sigma weight residual 180.00 -148.96 -31.04 0 5.00e+00 4.00e-02 3.85e+01 ... (remaining 7683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2258 0.063 - 0.125: 279 0.125 - 0.188: 5 0.188 - 0.250: 2 0.250 - 0.313: 1 Chirality restraints: 2545 Sorted by residual: chirality pdb=" CA LYS A2730 " pdb=" N LYS A2730 " pdb=" C LYS A2730 " pdb=" CB LYS A2730 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA GLN A2731 " pdb=" N GLN A2731 " pdb=" C GLN A2731 " pdb=" CB GLN A2731 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA SER A 139 " pdb=" N SER A 139 " pdb=" C SER A 139 " pdb=" CB SER A 139 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.63e-01 ... (remaining 2542 not shown) Planarity restraints: 2594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A2716 " 0.185 2.00e-02 2.50e+03 2.62e-01 6.89e+02 pdb=" C PRO A2716 " -0.413 2.00e-02 2.50e+03 pdb=" O PRO A2716 " 0.263 2.00e-02 2.50e+03 pdb=" N PHE A2718 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A2730 " 0.029 2.00e-02 2.50e+03 5.82e-02 3.39e+01 pdb=" C LYS A2730 " -0.101 2.00e-02 2.50e+03 pdb=" O LYS A2730 " 0.038 2.00e-02 2.50e+03 pdb=" N GLN A2731 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A2743 " -0.026 2.00e-02 2.50e+03 5.37e-02 2.88e+01 pdb=" C SER A2743 " 0.093 2.00e-02 2.50e+03 pdb=" O SER A2743 " -0.036 2.00e-02 2.50e+03 pdb=" N GLY A2744 " -0.031 2.00e-02 2.50e+03 ... (remaining 2591 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 567 2.71 - 3.25: 15866 3.25 - 3.80: 20613 3.80 - 4.35: 21217 4.35 - 4.90: 30252 Nonbonded interactions: 88515 Sorted by model distance: nonbonded pdb=" N SER A2000 " pdb=" O GLN A2002 " model vdw 2.158 3.120 nonbonded pdb=" O ASP A2715 " pdb=" N PHE A2718 " model vdw 2.191 3.120 nonbonded pdb=" O ILE A1112 " pdb=" N LEU A1116 " model vdw 2.203 3.120 nonbonded pdb=" O GLU A 714 " pdb=" N PHE A 718 " model vdw 2.211 3.120 nonbonded pdb=" O LYS A 163 " pdb=" N LYS A 200 " model vdw 2.238 3.120 ... (remaining 88510 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.150 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: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 38.730 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5372 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 : 0.015 1.624 12979 Z= 1.073 Angle : 0.921 52.115 18101 Z= 0.622 Chirality : 0.038 0.313 2545 Planarity : 0.006 0.262 2594 Dihedral : 6.952 47.839 2596 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.74 % Favored : 90.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.91 (0.16), residues: 2573 helix: 0.63 (0.13), residues: 1485 sheet: -2.83 (0.93), residues: 25 loop : -2.42 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 59 PHE 0.009 0.000 PHE A2051 TYR 0.000 0.000 TYR A 29 Details of bonding type rmsd hydrogen bonds : bond 0.18520 ( 1071) hydrogen bonds : angle 7.00508 ( 3165) covalent geometry : bond 0.01477 (12979) covalent geometry : angle 0.92131 (18101) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5146 Ramachandran restraints generated. 2573 Oldfield, 0 Emsley, 2573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5146 Ramachandran restraints generated. 2573 Oldfield, 0 Emsley, 2573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 2429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.591 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1214 time to fit residues: 14.3294 Evaluate side-chains 53 residues out of total 2429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 220 optimal weight: 10.0000 chunk 197 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 67 optimal weight: 20.0000 chunk 133 optimal weight: 2.9990 chunk 105 optimal weight: 30.0000 chunk 204 optimal weight: 20.0000 chunk 79 optimal weight: 8.9990 chunk 124 optimal weight: 30.0000 chunk 152 optimal weight: 8.9990 chunk 237 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.115167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.105839 restraints weight = 65862.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.105446 restraints weight = 101066.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.104705 restraints weight = 94808.781| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12979 Z= 0.315 Angle : 0.816 9.660 18101 Z= 0.522 Chirality : 0.043 0.217 2545 Planarity : 0.006 0.038 2594 Dihedral : 7.709 45.494 2593 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.79 % Favored : 89.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.30 % Twisted General : 0.36 % 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: -2.11 (0.15), residues: 2575 helix: -0.38 (0.12), residues: 1571 sheet: -3.53 (0.93), residues: 15 loop : -3.07 (0.18), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 59 PHE 0.031 0.000 PHE A2051 TYR 0.000 0.000 TYR A 29 Details of bonding type rmsd hydrogen bonds : bond 0.07358 ( 1071) hydrogen bonds : angle 6.87647 ( 3165) covalent geometry : bond 0.00428 (12979) covalent geometry : angle 0.81562 (18101) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 1.689 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1341 time to fit residues: 15.8692 Evaluate side-chains 54 residues out of total 2429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 140 optimal weight: 4.9990 chunk 100 optimal weight: 40.0000 chunk 153 optimal weight: 0.0980 chunk 119 optimal weight: 30.0000 chunk 6 optimal weight: 50.0000 chunk 23 optimal weight: 8.9990 chunk 210 optimal weight: 20.0000 chunk 170 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 chunk 226 optimal weight: 20.0000 overall best weight: 6.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.110774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.101235 restraints weight = 65482.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.099634 restraints weight = 97818.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.099758 restraints weight = 107874.427| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.8104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12979 Z= 0.283 Angle : 0.695 8.555 18101 Z= 0.447 Chirality : 0.042 0.194 2545 Planarity : 0.004 0.021 2594 Dihedral : 6.894 33.715 2593 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.65 % Favored : 88.12 % Rotamer: Outliers : 0.00 % Allowed : 50.00 % Favored : 50.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.77 (0.16), residues: 2575 helix: 0.05 (0.13), residues: 1576 sheet: -3.62 (0.90), residues: 16 loop : -3.25 (0.17), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 59 PHE 0.021 0.000 PHE A2051 TYR 0.000 0.000 TYR A 29 Details of bonding type rmsd hydrogen bonds : bond 0.06569 ( 1071) hydrogen bonds : angle 6.25030 ( 3165) covalent geometry : bond 0.00386 (12979) covalent geometry : angle 0.69457 (18101) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 2429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.424 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1236 time to fit residues: 14.5711 Evaluate side-chains 53 residues out of total 2429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 4 optimal weight: 80.0000 chunk 76 optimal weight: 30.0000 chunk 126 optimal weight: 8.9990 chunk 140 optimal weight: 1.9990 chunk 72 optimal weight: 30.0000 chunk 176 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 181 optimal weight: 0.0870 chunk 199 optimal weight: 7.9990 chunk 22 optimal weight: 50.0000 chunk 162 optimal weight: 10.0000 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.109788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.099019 restraints weight = 64783.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.098624 restraints weight = 104950.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.098421 restraints weight = 89033.094| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 0.9574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12979 Z= 0.209 Angle : 0.560 9.164 18101 Z= 0.356 Chirality : 0.040 0.174 2545 Planarity : 0.003 0.023 2594 Dihedral : 6.255 40.075 2593 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.52 % Favored : 89.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.04 (0.17), residues: 2575 helix: 0.64 (0.13), residues: 1612 sheet: -3.76 (0.87), residues: 14 loop : -3.12 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 59 PHE 0.033 0.001 PHE A2051 TYR 0.000 0.000 TYR A 29 Details of bonding type rmsd hydrogen bonds : bond 0.04722 ( 1071) hydrogen bonds : angle 5.53291 ( 3165) covalent geometry : bond 0.00290 (12979) covalent geometry : angle 0.55966 (18101) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 2429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.626 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1226 time to fit residues: 14.5944 Evaluate side-chains 53 residues out of total 2429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 242 optimal weight: 1.9990 chunk 225 optimal weight: 30.0000 chunk 196 optimal weight: 20.0000 chunk 169 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 145 optimal weight: 0.0870 chunk 36 optimal weight: 30.0000 chunk 48 optimal weight: 20.0000 chunk 234 optimal weight: 10.0000 chunk 82 optimal weight: 0.0770 chunk 117 optimal weight: 20.0000 overall best weight: 4.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.108764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.098738 restraints weight = 64738.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.097378 restraints weight = 96392.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.097179 restraints weight = 117378.817| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 1.0389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12979 Z= 0.177 Angle : 0.526 7.399 18101 Z= 0.333 Chirality : 0.039 0.159 2545 Planarity : 0.003 0.020 2594 Dihedral : 5.889 31.333 2593 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.52 % Favored : 89.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.77 (0.17), residues: 2575 helix: 0.88 (0.13), residues: 1612 sheet: -3.80 (0.88), residues: 14 loop : -3.06 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 59 PHE 0.017 0.000 PHE A2051 TYR 0.000 0.000 TYR A 29 Details of bonding type rmsd hydrogen bonds : bond 0.04517 ( 1071) hydrogen bonds : angle 5.33633 ( 3165) covalent geometry : bond 0.00240 (12979) covalent geometry : angle 0.52618 (18101) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 2429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.558 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1264 time to fit residues: 14.8538 Evaluate side-chains 53 residues out of total 2429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 47 optimal weight: 6.9990 chunk 92 optimal weight: 30.0000 chunk 193 optimal weight: 9.9990 chunk 20 optimal weight: 50.0000 chunk 117 optimal weight: 20.0000 chunk 174 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 162 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 52 optimal weight: 0.0980 chunk 95 optimal weight: 5.9990 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.108356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.097819 restraints weight = 65376.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.095570 restraints weight = 94854.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.095663 restraints weight = 113094.323| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 1.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12979 Z= 0.191 Angle : 0.524 7.691 18101 Z= 0.334 Chirality : 0.039 0.162 2545 Planarity : 0.003 0.020 2594 Dihedral : 5.916 31.586 2593 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.38 % Favored : 88.47 % Rotamer: Outliers : 0.00 % Allowed : 50.00 % Favored : 50.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.68 (0.17), residues: 2575 helix: 0.96 (0.13), residues: 1628 sheet: -3.95 (0.82), residues: 19 loop : -3.07 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 59 PHE 0.011 0.000 PHE A2051 TYR 0.000 0.000 TYR A 29 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 1071) hydrogen bonds : angle 5.34522 ( 3165) covalent geometry : bond 0.00257 (12979) covalent geometry : angle 0.52394 (18101) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 2429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.636 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1233 time to fit residues: 14.6938 Evaluate side-chains 53 residues out of total 2429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 198 optimal weight: 9.9990 chunk 65 optimal weight: 40.0000 chunk 258 optimal weight: 3.9990 chunk 217 optimal weight: 5.9990 chunk 80 optimal weight: 30.0000 chunk 232 optimal weight: 10.0000 chunk 166 optimal weight: 0.0040 chunk 78 optimal weight: 50.0000 chunk 63 optimal weight: 50.0000 chunk 103 optimal weight: 40.0000 chunk 60 optimal weight: 30.0000 overall best weight: 6.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.106055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.095254 restraints weight = 64600.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.094239 restraints weight = 116675.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.093801 restraints weight = 110601.199| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 1.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12979 Z= 0.244 Angle : 0.605 9.614 18101 Z= 0.390 Chirality : 0.040 0.164 2545 Planarity : 0.004 0.021 2594 Dihedral : 6.657 47.298 2593 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.62 % Favored : 87.22 % Rotamer: Outliers : 0.00 % Allowed : 50.00 % Favored : 50.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.13 (0.17), residues: 2575 helix: 0.61 (0.13), residues: 1614 sheet: -3.57 (0.94), residues: 23 loop : -3.22 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 59 PHE 0.045 0.001 PHE A2051 TYR 0.000 0.000 TYR A 29 Details of bonding type rmsd hydrogen bonds : bond 0.05235 ( 1071) hydrogen bonds : angle 5.94977 ( 3165) covalent geometry : bond 0.00336 (12979) covalent geometry : angle 0.60486 (18101) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 2429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.560 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1248 time to fit residues: 14.6983 Evaluate side-chains 53 residues out of total 2429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 254 optimal weight: 9.9990 chunk 238 optimal weight: 0.5980 chunk 200 optimal weight: 30.0000 chunk 173 optimal weight: 0.8980 chunk 15 optimal weight: 50.0000 chunk 105 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 chunk 45 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.109939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.099518 restraints weight = 64488.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.098795 restraints weight = 111006.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.098844 restraints weight = 111385.424| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 1.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.015 12979 Z= 0.097 Angle : 0.430 5.606 18101 Z= 0.265 Chirality : 0.038 0.149 2545 Planarity : 0.002 0.020 2594 Dihedral : 5.175 33.742 2593 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.23 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.17), residues: 2575 helix: 1.22 (0.13), residues: 1650 sheet: -3.46 (0.84), residues: 28 loop : -3.09 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 59 PHE 0.007 0.000 PHE A2051 TYR 0.000 0.000 TYR A 29 Details of bonding type rmsd hydrogen bonds : bond 0.03223 ( 1071) hydrogen bonds : angle 4.67688 ( 3165) covalent geometry : bond 0.00131 (12979) covalent geometry : angle 0.43016 (18101) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 1.460 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1339 time to fit residues: 15.5662 Evaluate side-chains 53 residues out of total 2429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 81 optimal weight: 30.0000 chunk 8 optimal weight: 40.0000 chunk 206 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 246 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 51 optimal weight: 30.0000 chunk 252 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 226 optimal weight: 0.0030 overall best weight: 5.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.105940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.094705 restraints weight = 64413.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.093469 restraints weight = 123719.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.093650 restraints weight = 122648.685| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 1.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12979 Z= 0.239 Angle : 0.578 8.205 18101 Z= 0.373 Chirality : 0.040 0.168 2545 Planarity : 0.003 0.024 2594 Dihedral : 6.185 39.744 2593 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.50 % Favored : 87.34 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.17), residues: 2575 helix: 0.89 (0.13), residues: 1637 sheet: -3.31 (0.95), residues: 28 loop : -3.21 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 59 PHE 0.012 0.000 PHE A2051 TYR 0.000 0.000 TYR A 29 Details of bonding type rmsd hydrogen bonds : bond 0.05008 ( 1071) hydrogen bonds : angle 5.65826 ( 3165) covalent geometry : bond 0.00323 (12979) covalent geometry : angle 0.57795 (18101) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 1.577 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1215 time to fit residues: 14.6178 Evaluate side-chains 53 residues out of total 2429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 145 optimal weight: 4.9990 chunk 56 optimal weight: 0.0000 chunk 206 optimal weight: 20.0000 chunk 229 optimal weight: 10.0000 chunk 29 optimal weight: 30.0000 chunk 251 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 175 optimal weight: 0.6980 chunk 10 optimal weight: 20.0000 chunk 58 optimal weight: 50.0000 chunk 18 optimal weight: 9.9990 overall best weight: 4.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.106955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.096044 restraints weight = 63815.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.094023 restraints weight = 101843.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.094226 restraints weight = 120208.205| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 1.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 12979 Z= 0.176 Angle : 0.505 6.508 18101 Z= 0.321 Chirality : 0.039 0.156 2545 Planarity : 0.003 0.021 2594 Dihedral : 5.757 39.523 2593 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.15 % Favored : 88.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.69 (0.17), residues: 2575 helix: 1.01 (0.13), residues: 1654 sheet: -3.45 (0.90), residues: 29 loop : -3.34 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 59 PHE 0.010 0.000 PHE A2051 TYR 0.000 0.000 TYR A 29 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 1071) hydrogen bonds : angle 5.22582 ( 3165) covalent geometry : bond 0.00239 (12979) covalent geometry : angle 0.50533 (18101) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 1.726 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1725 time to fit residues: 20.2715 Evaluate side-chains 53 residues out of total 2429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 1 optimal weight: 100.0000 chunk 103 optimal weight: 50.0000 chunk 205 optimal weight: 20.0000 chunk 259 optimal weight: 3.9990 chunk 25 optimal weight: 30.0000 chunk 90 optimal weight: 50.0000 chunk 59 optimal weight: 40.0000 chunk 157 optimal weight: 0.7980 chunk 14 optimal weight: 50.0000 chunk 24 optimal weight: 30.0000 chunk 244 optimal weight: 6.9990 overall best weight: 12.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.101566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.091612 restraints weight = 64105.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.091484 restraints weight = 123337.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.090785 restraints weight = 110326.705| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 1.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 12979 Z= 0.448 Angle : 0.857 10.757 18101 Z= 0.563 Chirality : 0.046 0.263 2545 Planarity : 0.005 0.031 2594 Dihedral : 8.232 52.213 2593 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.35 % Allowed : 16.12 % Favored : 83.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.55 (0.16), residues: 2575 helix: -0.56 (0.12), residues: 1583 sheet: -3.87 (0.90), residues: 25 loop : -3.61 (0.18), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 59 PHE 0.030 0.000 PHE A2051 TYR 0.000 0.000 TYR A 29 Details of bonding type rmsd hydrogen bonds : bond 0.07339 ( 1071) hydrogen bonds : angle 7.39851 ( 3165) covalent geometry : bond 0.00612 (12979) covalent geometry : angle 0.85682 (18101) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3205.28 seconds wall clock time: 55 minutes 44.85 seconds (3344.85 seconds total)