Starting phenix.real_space_refine on Wed Jan 14 20:03:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fo2_29339/01_2026/8fo2_29339_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fo2_29339/01_2026/8fo2_29339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fo2_29339/01_2026/8fo2_29339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fo2_29339/01_2026/8fo2_29339.map" model { file = "/net/cci-nas-00/data/ceres_data/8fo2_29339/01_2026/8fo2_29339_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fo2_29339/01_2026/8fo2_29339_neut.cif" } resolution = 4.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.041 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 8 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 11649 2.51 5 N 3136 2.21 5 O 3348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18255 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1115 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 167} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 10, 'ARG:plan': 10, 'GLN:plan1': 4, 'PHE:plan': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'GLU:plan': 8, 'ASN:plan1': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 192 Chain: "E" Number of atoms: 17048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2275, 17048 Classifications: {'peptide': 2275} Incomplete info: {'truncation_to_alanine': 274} Link IDs: {'PCIS': 1, 'PTRANS': 84, 'TRANS': 2189} Chain breaks: 18 Unresolved non-hydrogen bonds: 1055 Unresolved non-hydrogen angles: 1293 Unresolved non-hydrogen dihedrals: 885 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLU:plan': 51, 'ASN:plan1': 14, 'GLN:plan1': 17, 'ASP:plan': 24, 'PHE:plan': 11, 'TYR:plan': 5, 'HIS:plan': 12, 'ARG:plan': 15, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 631 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.25, per 1000 atoms: 0.23 Number of scatterers: 18255 At special positions: 0 Unit cell: (98.58, 132.5, 245.92, 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 113 16.00 P 8 15.00 Mg 1 11.99 O 3348 8.00 N 3136 7.00 C 11649 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: 1.64 Conformation dependent library (CDL) restraints added in 955.0 milliseconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4676 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 19 sheets defined 45.0% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'B' and resid 19 through 28 removed outlier: 3.657A pdb=" N LEU B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 4.270A pdb=" N TYR B 78 " --> pdb=" O THR B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 109 removed outlier: 3.573A pdb=" N PHE B 96 " --> pdb=" O ASN B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 146 removed outlier: 3.945A pdb=" N ARG B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE B 142 " --> pdb=" O GLN B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 176 removed outlier: 3.506A pdb=" N ASN B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 24 Processing helix chain 'E' and resid 28 through 44 Processing helix chain 'E' and resid 57 through 60 Processing helix chain 'E' and resid 61 through 71 Processing helix chain 'E' and resid 74 through 92 removed outlier: 3.721A pdb=" N GLN E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP E 82 " --> pdb=" O GLN E 78 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER E 83 " --> pdb=" O GLN E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 100 Processing helix chain 'E' and resid 114 through 125 removed outlier: 3.946A pdb=" N HIS E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 143 removed outlier: 3.671A pdb=" N ILE E 134 " --> pdb=" O ASN E 130 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 154 Processing helix chain 'E' and resid 158 through 167 Processing helix chain 'E' and resid 173 through 181 Processing helix chain 'E' and resid 186 through 190 removed outlier: 4.083A pdb=" N ARG E 190 " --> pdb=" O LEU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 203 removed outlier: 3.630A pdb=" N GLU E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN E 202 " --> pdb=" O GLU E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 212 Processing helix chain 'E' and resid 218 through 233 Processing helix chain 'E' and resid 237 through 243 removed outlier: 4.326A pdb=" N VAL E 241 " --> pdb=" O ASN E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 258 Processing helix chain 'E' and resid 263 through 277 Processing helix chain 'E' and resid 284 through 302 Processing helix chain 'E' and resid 308 through 325 removed outlier: 3.812A pdb=" N LEU E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 360 Processing helix chain 'E' and resid 363 through 381 removed outlier: 3.530A pdb=" N GLN E 367 " --> pdb=" O ASN E 363 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR E 380 " --> pdb=" O ASN E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 386 removed outlier: 4.377A pdb=" N GLU E 386 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 408 removed outlier: 3.894A pdb=" N GLU E 400 " --> pdb=" O PRO E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 429 removed outlier: 3.751A pdb=" N PHE E 415 " --> pdb=" O SER E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 440 Processing helix chain 'E' and resid 441 through 452 Processing helix chain 'E' and resid 455 through 471 removed outlier: 3.960A pdb=" N ALA E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 494 Proline residue: E 485 - end of helix Processing helix chain 'E' and resid 497 through 513 removed outlier: 4.409A pdb=" N VAL E 513 " --> pdb=" O LEU E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 540 removed outlier: 3.662A pdb=" N MET E 532 " --> pdb=" O HIS E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 553 Processing helix chain 'E' and resid 556 through 572 removed outlier: 4.096A pdb=" N GLN E 560 " --> pdb=" O ASN E 556 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS E 572 " --> pdb=" O SER E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 584 removed outlier: 4.008A pdb=" N MET E 579 " --> pdb=" O ASP E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 596 removed outlier: 3.864A pdb=" N SER E 588 " --> pdb=" O GLY E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 614 removed outlier: 3.628A pdb=" N GLY E 611 " --> pdb=" O LEU E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 619 removed outlier: 3.741A pdb=" N VAL E 619 " --> pdb=" O LYS E 616 " (cutoff:3.500A) Processing helix chain 'E' and resid 623 through 638 Processing helix chain 'E' and resid 641 through 659 Processing helix chain 'E' and resid 671 through 685 removed outlier: 3.553A pdb=" N ILE E 675 " --> pdb=" O PHE E 671 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS E 677 " --> pdb=" O LEU E 673 " (cutoff:3.500A) Processing helix chain 'E' and resid 688 through 704 removed outlier: 4.005A pdb=" N MET E 704 " --> pdb=" O ALA E 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 705 through 719 removed outlier: 3.770A pdb=" N LYS E 709 " --> pdb=" O ASP E 705 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN E 719 " --> pdb=" O ARG E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 721 through 732 removed outlier: 3.975A pdb=" N GLU E 726 " --> pdb=" O SER E 722 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N CYS E 727 " --> pdb=" O ILE E 723 " (cutoff:3.500A) Processing helix chain 'E' and resid 743 through 751 Processing helix chain 'E' and resid 754 through 764 removed outlier: 3.729A pdb=" N VAL E 758 " --> pdb=" O SER E 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 767 through 781 Processing helix chain 'E' and resid 783 through 795 removed outlier: 3.871A pdb=" N ARG E 793 " --> pdb=" O LEU E 789 " (cutoff:3.500A) Processing helix chain 'E' and resid 834 through 851 Processing helix chain 'E' and resid 997 through 1002 removed outlier: 3.645A pdb=" N SER E1001 " --> pdb=" O ILE E 997 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN E1002 " --> pdb=" O ASP E 998 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 997 through 1002' Processing helix chain 'E' and resid 1006 through 1010 removed outlier: 3.622A pdb=" N LEU E1010 " --> pdb=" O SER E1007 " (cutoff:3.500A) Processing helix chain 'E' and resid 1027 through 1032 removed outlier: 3.939A pdb=" N CYS E1031 " --> pdb=" O PRO E1027 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU E1032 " --> pdb=" O GLN E1028 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1027 through 1032' Processing helix chain 'E' and resid 1053 through 1057 Processing helix chain 'E' and resid 1190 through 1195 removed outlier: 3.584A pdb=" N LEU E1195 " --> pdb=" O ILE E1192 " (cutoff:3.500A) Processing helix chain 'E' and resid 1213 through 1217 removed outlier: 3.820A pdb=" N TRP E1217 " --> pdb=" O PRO E1214 " (cutoff:3.500A) Processing helix chain 'E' and resid 1240 through 1245 removed outlier: 3.836A pdb=" N LEU E1243 " --> pdb=" O LYS E1240 " (cutoff:3.500A) Processing helix chain 'E' and resid 1261 through 1267 removed outlier: 3.560A pdb=" N ILE E1264 " --> pdb=" O PRO E1261 " (cutoff:3.500A) Processing helix chain 'E' and resid 1285 through 1291 removed outlier: 3.866A pdb=" N MET E1288 " --> pdb=" O PRO E1285 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS E1290 " --> pdb=" O GLU E1287 " (cutoff:3.500A) Processing helix chain 'E' and resid 1316 through 1328 removed outlier: 3.631A pdb=" N ARG E1320 " --> pdb=" O LYS E1316 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS E1328 " --> pdb=" O GLN E1324 " (cutoff:3.500A) Processing helix chain 'E' and resid 1347 through 1355 removed outlier: 3.672A pdb=" N GLN E1352 " --> pdb=" O THR E1348 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN E1353 " --> pdb=" O THR E1349 " (cutoff:3.500A) Processing helix chain 'E' and resid 1398 through 1402 Processing helix chain 'E' and resid 1404 through 1408 Processing helix chain 'E' and resid 1420 through 1424 removed outlier: 3.501A pdb=" N GLY E1424 " --> pdb=" O LEU E1421 " (cutoff:3.500A) Processing helix chain 'E' and resid 1426 through 1431 removed outlier: 3.847A pdb=" N ALA E1430 " --> pdb=" O ALA E1426 " (cutoff:3.500A) Processing helix chain 'E' and resid 1431 through 1442 Processing helix chain 'E' and resid 1465 through 1473 removed outlier: 4.196A pdb=" N ILE E1469 " --> pdb=" O CYS E1465 " (cutoff:3.500A) Processing helix chain 'E' and resid 1494 through 1509 Processing helix chain 'E' and resid 1517 through 1520 Processing helix chain 'E' and resid 1525 through 1538 Processing helix chain 'E' and resid 1550 through 1560 removed outlier: 3.619A pdb=" N ASN E1560 " --> pdb=" O LEU E1556 " (cutoff:3.500A) Processing helix chain 'E' and resid 1568 through 1578 removed outlier: 3.987A pdb=" N HIS E1574 " --> pdb=" O PRO E1570 " (cutoff:3.500A) Processing helix chain 'E' and resid 1599 through 1612 removed outlier: 3.875A pdb=" N LEU E1603 " --> pdb=" O GLU E1599 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA E1608 " --> pdb=" O CYS E1604 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN E1609 " --> pdb=" O LYS E1605 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE E1610 " --> pdb=" O ILE E1606 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU E1611 " --> pdb=" O MET E1607 " (cutoff:3.500A) Processing helix chain 'E' and resid 1644 through 1654 removed outlier: 3.561A pdb=" N GLN E1648 " --> pdb=" O ASN E1644 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE E1650 " --> pdb=" O MET E1646 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS E1651 " --> pdb=" O THR E1647 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU E1652 " --> pdb=" O GLN E1648 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU E1654 " --> pdb=" O PHE E1650 " (cutoff:3.500A) Processing helix chain 'E' and resid 1704 through 1713 removed outlier: 4.064A pdb=" N ASN E1710 " --> pdb=" O SER E1706 " (cutoff:3.500A) Processing helix chain 'E' and resid 1770 through 1792 removed outlier: 3.557A pdb=" N ILE E1775 " --> pdb=" O ARG E1771 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N HIS E1783 " --> pdb=" O GLN E1779 " (cutoff:3.500A) Processing helix chain 'E' and resid 1829 through 1835 Processing helix chain 'E' and resid 1852 through 1856 Processing helix chain 'E' and resid 1865 through 1869 Processing helix chain 'E' and resid 1913 through 1925 removed outlier: 4.220A pdb=" N VAL E1923 " --> pdb=" O GLN E1919 " (cutoff:3.500A) Processing helix chain 'E' and resid 1954 through 1962 removed outlier: 3.563A pdb=" N LEU E1958 " --> pdb=" O SER E1954 " (cutoff:3.500A) Processing helix chain 'E' and resid 1969 through 1988 removed outlier: 3.539A pdb=" N ARG E1973 " --> pdb=" O THR E1969 " (cutoff:3.500A) Processing helix chain 'E' and resid 1996 through 1998 No H-bonds generated for 'chain 'E' and resid 1996 through 1998' Processing helix chain 'E' and resid 2017 through 2026 removed outlier: 3.859A pdb=" N ALA E2021 " --> pdb=" O ASP E2017 " (cutoff:3.500A) Processing helix chain 'E' and resid 2040 through 2046 Processing helix chain 'E' and resid 2051 through 2069 removed outlier: 4.296A pdb=" N ASP E2055 " --> pdb=" O ASN E2051 " (cutoff:3.500A) Processing helix chain 'E' and resid 2070 through 2077 removed outlier: 3.853A pdb=" N VAL E2074 " --> pdb=" O GLY E2070 " (cutoff:3.500A) Processing helix chain 'E' and resid 2094 through 2099 Processing helix chain 'E' and resid 2104 through 2106 No H-bonds generated for 'chain 'E' and resid 2104 through 2106' Processing helix chain 'E' and resid 2107 through 2115 Processing helix chain 'E' and resid 2125 through 2126 No H-bonds generated for 'chain 'E' and resid 2125 through 2126' Processing helix chain 'E' and resid 2128 through 2130 No H-bonds generated for 'chain 'E' and resid 2128 through 2130' Processing helix chain 'E' and resid 2135 through 2139 removed outlier: 3.795A pdb=" N CYS E2139 " --> pdb=" O ALA E2135 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2135 through 2139' Processing helix chain 'E' and resid 2277 through 2282 removed outlier: 4.074A pdb=" N VAL E2280 " --> pdb=" O ASP E2277 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS E2281 " --> pdb=" O LYS E2278 " (cutoff:3.500A) Processing helix chain 'E' and resid 2346 through 2351 removed outlier: 4.225A pdb=" N SER E2350 " --> pdb=" O TYR E2346 " (cutoff:3.500A) Processing helix chain 'E' and resid 2389 through 2394 removed outlier: 3.600A pdb=" N ARG E2394 " --> pdb=" O VAL E2390 " (cutoff:3.500A) Processing helix chain 'E' and resid 2499 through 2523 removed outlier: 3.808A pdb=" N GLN E2505 " --> pdb=" O PRO E2501 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU E2508 " --> pdb=" O VAL E2504 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS E2509 " --> pdb=" O GLN E2505 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU E2512 " --> pdb=" O GLU E2508 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG E2523 " --> pdb=" O GLU E2519 " (cutoff:3.500A) Processing helix chain 'E' and resid 2524 through 2526 No H-bonds generated for 'chain 'E' and resid 2524 through 2526' Processing sheet with id=AA1, first strand: chain 'B' and resid 43 through 52 removed outlier: 3.820A pdb=" N ASP B 43 " --> pdb=" O ASP B 63 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP B 51 " --> pdb=" O GLU B 55 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLU B 55 " --> pdb=" O TRP B 51 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N CYS B 84 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N LEU B 123 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE B 86 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU B 122 " --> pdb=" O THR B 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 1016 through 1017 removed outlier: 6.659A pdb=" N LEU E1016 " --> pdb=" O ASP E1041 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 1063 through 1064 removed outlier: 7.126A pdb=" N LEU E1063 " --> pdb=" O ASN E1089 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE E1113 " --> pdb=" O PHE E1088 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN E1135 " --> pdb=" O LEU E1112 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 1177 through 1179 removed outlier: 7.032A pdb=" N LEU E1201 " --> pdb=" O LEU E1226 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS E1251 " --> pdb=" O LEU E1225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 1329 through 1332 removed outlier: 3.816A pdb=" N GLN E1521 " --> pdb=" O TYR E1332 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 1373 through 1380 removed outlier: 3.514A pdb=" N LEU E1390 " --> pdb=" O TRP E1376 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET E1335 " --> pdb=" O VAL E1389 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP E1393 " --> pdb=" O LEU E1337 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N LEU E1414 " --> pdb=" O ARG E1334 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS E1336 " --> pdb=" O LEU E1414 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU E1416 " --> pdb=" O LYS E1336 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N MET E1338 " --> pdb=" O LEU E1416 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N VAL E1418 " --> pdb=" O MET E1338 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N ILE E1448 " --> pdb=" O ALA E1413 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR E1415 " --> pdb=" O ILE E1448 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N VAL E1450 " --> pdb=" O TYR E1415 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ALA E1417 " --> pdb=" O VAL E1450 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL E1447 " --> pdb=" O ASP E1484 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N HIS E1486 " --> pdb=" O VAL E1447 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU E1449 " --> pdb=" O HIS E1486 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 1547 through 1549 Processing sheet with id=AA8, first strand: chain 'E' and resid 1690 through 1692 removed outlier: 6.950A pdb=" N TYR E1747 " --> pdb=" O PRO E1768 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N CYS E1748 " --> pdb=" O ASN E1741 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ASN E1741 " --> pdb=" O CYS E1748 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 1811 through 1814 Processing sheet with id=AB1, first strand: chain 'E' and resid 1840 through 1841 Processing sheet with id=AB2, first strand: chain 'E' and resid 1893 through 1898 removed outlier: 3.912A pdb=" N LEU E1945 " --> pdb=" O LYS E1906 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA E1937 " --> pdb=" O VAL E1946 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLU E1948 " --> pdb=" O LEU E1935 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU E1935 " --> pdb=" O GLU E1948 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 2000 through 2002 Processing sheet with id=AB4, first strand: chain 'E' and resid 2140 through 2145 removed outlier: 6.308A pdb=" N LEU E2140 " --> pdb=" O ASP E2497 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP E2497 " --> pdb=" O LEU E2140 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG E2142 " --> pdb=" O VAL E2495 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS E2467 " --> pdb=" O LEU E2463 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU E2463 " --> pdb=" O LYS E2467 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL E2457 " --> pdb=" O LEU E2473 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 2155 through 2157 Processing sheet with id=AB6, first strand: chain 'E' and resid 2199 through 2207 removed outlier: 3.717A pdb=" N GLU E2212 " --> pdb=" O LEU E2207 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL E2226 " --> pdb=" O HIS E2236 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS E2236 " --> pdb=" O VAL E2226 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 2245 through 2250 removed outlier: 5.836A pdb=" N GLY E2266 " --> pdb=" O THR E2246 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU E2248 " --> pdb=" O LEU E2264 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU E2264 " --> pdb=" O LEU E2248 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA E2273 " --> pdb=" O VAL E2265 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR E2267 " --> pdb=" O LYS E2271 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS E2271 " --> pdb=" O THR E2267 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 2315 through 2319 Processing sheet with id=AB9, first strand: chain 'E' and resid 2354 through 2359 removed outlier: 6.797A pdb=" N ALA E2366 " --> pdb=" O ILE E2355 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL E2357 " --> pdb=" O TYR E2364 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR E2364 " --> pdb=" O VAL E2357 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LYS E2367 " --> pdb=" O VAL E2372 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL E2372 " --> pdb=" O LYS E2367 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 2414 through 2419 removed outlier: 6.690A pdb=" N GLY E2428 " --> pdb=" O LYS E2415 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU E2417 " --> pdb=" O TRP E2426 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N TRP E2426 " --> pdb=" O LEU E2417 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU E2436 " --> pdb=" O ARG E2446 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG E2446 " --> pdb=" O LEU E2436 " (cutoff:3.500A) 754 hydrogen bonds defined for protein. 2136 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: 4.74 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5854 1.34 - 1.46: 3549 1.46 - 1.58: 8993 1.58 - 1.70: 12 1.70 - 1.82: 165 Bond restraints: 18573 Sorted by residual: bond pdb=" N3B GNP B 202 " pdb=" PG GNP B 202 " ideal model delta sigma weight residual 1.801 1.617 0.184 2.00e-02 2.50e+03 8.45e+01 bond pdb=" O3A GNP B 202 " pdb=" PB GNP B 202 " ideal model delta sigma weight residual 1.687 1.594 0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" N3B GNP B 202 " pdb=" PB GNP B 202 " ideal model delta sigma weight residual 1.681 1.607 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" N LYS B 126 " pdb=" CA LYS B 126 " ideal model delta sigma weight residual 1.457 1.503 -0.045 1.29e-02 6.01e+03 1.23e+01 bond pdb=" N ASN E 173 " pdb=" CA ASN E 173 " ideal model delta sigma weight residual 1.454 1.496 -0.042 1.27e-02 6.20e+03 1.09e+01 ... (remaining 18568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 24894 2.99 - 5.99: 318 5.99 - 8.98: 50 8.98 - 11.97: 11 11.97 - 14.97: 3 Bond angle restraints: 25276 Sorted by residual: angle pdb=" N ALA E 183 " pdb=" CA ALA E 183 " pdb=" C ALA E 183 " ideal model delta sigma weight residual 109.14 94.17 14.97 1.49e+00 4.50e-01 1.01e+02 angle pdb=" N LYS E 182 " pdb=" CA LYS E 182 " pdb=" C LYS E 182 " ideal model delta sigma weight residual 113.51 100.11 13.40 1.52e+00 4.33e-01 7.77e+01 angle pdb=" N GLY E 180 " pdb=" CA GLY E 180 " pdb=" C GLY E 180 " ideal model delta sigma weight residual 112.73 104.82 7.91 1.20e+00 6.94e-01 4.34e+01 angle pdb=" CA ALA E 183 " pdb=" C ALA E 183 " pdb=" O ALA E 183 " ideal model delta sigma weight residual 121.51 114.23 7.28 1.12e+00 7.97e-01 4.22e+01 angle pdb=" CA CYS E 181 " pdb=" C CYS E 181 " pdb=" O CYS E 181 " ideal model delta sigma weight residual 121.72 114.69 7.03 1.18e+00 7.18e-01 3.55e+01 ... (remaining 25271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.29: 10951 31.29 - 62.59: 261 62.59 - 93.88: 36 93.88 - 125.18: 0 125.18 - 156.47: 4 Dihedral angle restraints: 11252 sinusoidal: 4099 harmonic: 7153 Sorted by residual: dihedral pdb=" CA TRP E2104 " pdb=" C TRP E2104 " pdb=" N PRO E2105 " pdb=" CA PRO E2105 " ideal model delta harmonic sigma weight residual -180.00 -150.26 -29.74 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA GLN E1845 " pdb=" C GLN E1845 " pdb=" N PRO E1846 " pdb=" CA PRO E1846 " ideal model delta harmonic sigma weight residual -180.00 -151.88 -28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ASN E 284 " pdb=" C ASN E 284 " pdb=" N ILE E 285 " pdb=" CA ILE E 285 " ideal model delta harmonic sigma weight residual -180.00 -155.38 -24.62 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 11249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.124: 3067 1.124 - 2.248: 0 2.248 - 3.371: 0 3.371 - 4.495: 0 4.495 - 5.619: 1 Chirality restraints: 3068 Sorted by residual: chirality pdb=" C3' GNP B 202 " pdb=" C2' GNP B 202 " pdb=" C4' GNP B 202 " pdb=" O3' GNP B 202 " both_signs ideal model delta sigma weight residual False -2.71 2.91 -5.62 2.00e-01 2.50e+01 7.89e+02 chirality pdb=" CB ILE E1715 " pdb=" CA ILE E1715 " pdb=" CG1 ILE E1715 " pdb=" CG2 ILE E1715 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA ALA E 183 " pdb=" N ALA E 183 " pdb=" C ALA E 183 " pdb=" CB ALA E 183 " both_signs ideal model delta sigma weight residual False 2.48 2.81 -0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 3065 not shown) Planarity restraints: 3177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 571 " 0.037 2.00e-02 2.50e+03 7.24e-02 5.24e+01 pdb=" C VAL E 571 " -0.125 2.00e-02 2.50e+03 pdb=" O VAL E 571 " 0.046 2.00e-02 2.50e+03 pdb=" N HIS E 572 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E1327 " 0.021 2.00e-02 2.50e+03 4.19e-02 1.76e+01 pdb=" C LYS E1327 " -0.073 2.00e-02 2.50e+03 pdb=" O LYS E1327 " 0.028 2.00e-02 2.50e+03 pdb=" N LYS E1328 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E1983 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C ARG E1983 " 0.067 2.00e-02 2.50e+03 pdb=" O ARG E1983 " -0.025 2.00e-02 2.50e+03 pdb=" N TYR E1984 " -0.023 2.00e-02 2.50e+03 ... (remaining 3174 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 27 2.35 - 2.99: 9250 2.99 - 3.63: 27499 3.63 - 4.26: 38638 4.26 - 4.90: 63668 Nonbonded interactions: 139082 Sorted by model distance: nonbonded pdb="MG MG B 201 " pdb=" O2B GNP B 202 " model vdw 1.718 2.170 nonbonded pdb="MG MG B 201 " pdb=" O3G GNP B 202 " model vdw 1.944 2.170 nonbonded pdb=" OG1 THR B 39 " pdb="MG MG B 201 " model vdw 2.099 2.170 nonbonded pdb=" N ALA E 183 " pdb=" O ALA E 183 " model vdw 2.154 2.496 nonbonded pdb=" NZ LYS B 20 " pdb=" O1G GNP B 202 " model vdw 2.213 3.120 ... (remaining 139077 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 7.310 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.390 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 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 : 0.004 0.184 18573 Z= 0.232 Angle : 0.896 14.968 25276 Z= 0.491 Chirality : 0.114 5.619 3068 Planarity : 0.006 0.072 3177 Dihedral : 14.555 156.473 6576 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.10 % Favored : 92.73 % Rotamer: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.18), residues: 2408 helix: 0.53 (0.18), residues: 952 sheet: -1.51 (0.30), residues: 331 loop : -1.77 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E2026 TYR 0.022 0.002 TYR E1992 PHE 0.030 0.002 PHE E2344 TRP 0.042 0.003 TRP E2104 HIS 0.007 0.001 HIS E1584 Details of bonding type rmsd covalent geometry : bond 0.00415 (18573) covalent geometry : angle 0.89603 (25276) hydrogen bonds : bond 0.16003 ( 754) hydrogen bonds : angle 6.40175 ( 2136) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: B 20 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7331 (mtpp) REVERT: E 2459 MET cc_start: 0.7668 (ppp) cc_final: 0.7302 (ppp) REVERT: E 2470 MET cc_start: 0.7780 (mmm) cc_final: 0.7549 (mmm) REVERT: E 2521 MET cc_start: 0.7464 (ptp) cc_final: 0.7161 (ptp) outliers start: 3 outliers final: 0 residues processed: 155 average time/residue: 0.1096 time to fit residues: 29.0722 Evaluate side-chains 107 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 309 GLN ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 444 ASN E1021 ASN E1029 GLN E1972 HIS E2113 GLN ** E2173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2510 HIS ** 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 = 0.3767 r_free = 0.3767 target = 0.084768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.065782 restraints weight = 81380.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.065437 restraints weight = 49442.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.066194 restraints weight = 42602.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.066585 restraints weight = 32685.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.066773 restraints weight = 31251.840| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18573 Z= 0.140 Angle : 0.615 8.597 25276 Z= 0.312 Chirality : 0.042 0.186 3068 Planarity : 0.004 0.062 3177 Dihedral : 8.112 76.343 2630 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.05 % Allowed : 4.57 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.18), residues: 2408 helix: 0.81 (0.17), residues: 975 sheet: -1.37 (0.29), residues: 331 loop : -1.81 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 767 TYR 0.014 0.001 TYR E1992 PHE 0.027 0.001 PHE E 188 TRP 0.025 0.001 TRP E2104 HIS 0.006 0.001 HIS E 452 Details of bonding type rmsd covalent geometry : bond 0.00305 (18573) covalent geometry : angle 0.61500 (25276) hydrogen bonds : bond 0.04138 ( 754) hydrogen bonds : angle 5.02703 ( 2136) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LEU cc_start: 0.9034 (mm) cc_final: 0.8780 (mm) REVERT: B 87 MET cc_start: 0.5182 (tmm) cc_final: 0.4769 (tmm) REVERT: B 173 MET cc_start: 0.8821 (tmm) cc_final: 0.8536 (tmm) REVERT: E 188 PHE cc_start: 0.8862 (m-80) cc_final: 0.8523 (m-10) REVERT: E 273 LEU cc_start: 0.8956 (mm) cc_final: 0.8735 (mm) REVERT: E 2106 MET cc_start: 0.8837 (ppp) cc_final: 0.8573 (ppp) outliers start: 1 outliers final: 1 residues processed: 132 average time/residue: 0.1107 time to fit residues: 24.9413 Evaluate side-chains 100 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 138 optimal weight: 0.8980 chunk 177 optimal weight: 6.9990 chunk 139 optimal weight: 0.2980 chunk 190 optimal weight: 0.6980 chunk 205 optimal weight: 0.0970 chunk 120 optimal weight: 0.2980 chunk 124 optimal weight: 0.0980 chunk 130 optimal weight: 0.8980 chunk 25 optimal weight: 0.0050 chunk 90 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 overall best weight: 0.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1710 ASN ** E2173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.086216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.067452 restraints weight = 81720.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.067275 restraints weight = 47697.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.068063 restraints weight = 42321.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.068436 restraints weight = 32333.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.068634 restraints weight = 30560.021| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18573 Z= 0.100 Angle : 0.566 8.695 25276 Z= 0.284 Chirality : 0.041 0.151 3068 Planarity : 0.004 0.056 3177 Dihedral : 7.708 70.034 2630 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.18), residues: 2408 helix: 0.99 (0.17), residues: 979 sheet: -1.15 (0.30), residues: 322 loop : -1.70 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E2026 TYR 0.016 0.001 TYR E1992 PHE 0.021 0.001 PHE E1700 TRP 0.022 0.001 TRP E1376 HIS 0.006 0.001 HIS E1986 Details of bonding type rmsd covalent geometry : bond 0.00207 (18573) covalent geometry : angle 0.56581 (25276) hydrogen bonds : bond 0.03318 ( 754) hydrogen bonds : angle 4.51234 ( 2136) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LEU cc_start: 0.8999 (mm) cc_final: 0.8774 (mm) REVERT: E 188 PHE cc_start: 0.8760 (m-80) cc_final: 0.8457 (m-10) REVERT: E 273 LEU cc_start: 0.8934 (mm) cc_final: 0.8703 (mm) REVERT: E 1203 MET cc_start: 0.8496 (mmt) cc_final: 0.7987 (mmm) REVERT: E 2315 MET cc_start: 0.8009 (mmm) cc_final: 0.7800 (mmm) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1106 time to fit residues: 26.7945 Evaluate side-chains 108 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 212 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 220 optimal weight: 8.9990 chunk 163 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 213 optimal weight: 0.0980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 677 HIS E 678 GLN E1002 GLN E1029 GLN ** E1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1710 ASN ** E2173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.084205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.065307 restraints weight = 80339.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.064567 restraints weight = 51017.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.065448 restraints weight = 44938.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.065650 restraints weight = 33770.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.065988 restraints weight = 32720.799| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18573 Z= 0.159 Angle : 0.592 7.950 25276 Z= 0.300 Chirality : 0.041 0.173 3068 Planarity : 0.004 0.066 3177 Dihedral : 7.616 66.109 2630 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.18), residues: 2408 helix: 1.03 (0.18), residues: 972 sheet: -1.38 (0.30), residues: 323 loop : -1.68 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E2176 TYR 0.013 0.001 TYR B 27 PHE 0.017 0.002 PHE E1047 TRP 0.032 0.002 TRP E2104 HIS 0.006 0.001 HIS E1043 Details of bonding type rmsd covalent geometry : bond 0.00363 (18573) covalent geometry : angle 0.59231 (25276) hydrogen bonds : bond 0.03284 ( 754) hydrogen bonds : angle 4.50690 ( 2136) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 28 SER cc_start: 0.7604 (t) cc_final: 0.7325 (p) REVERT: B 87 MET cc_start: 0.4411 (tmm) cc_final: 0.4033 (tmm) REVERT: E 188 PHE cc_start: 0.8818 (m-80) cc_final: 0.8557 (m-10) REVERT: E 586 MET cc_start: 0.8462 (mmm) cc_final: 0.7926 (mmp) REVERT: E 1203 MET cc_start: 0.8734 (mmt) cc_final: 0.8270 (mmm) REVERT: E 2106 MET cc_start: 0.8870 (ppp) cc_final: 0.8341 (tmm) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1118 time to fit residues: 25.7110 Evaluate side-chains 105 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 81 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 190 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 238 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 251 ASN ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1101 ASN ** E2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.083581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.064610 restraints weight = 81042.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.064061 restraints weight = 49514.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.064852 restraints weight = 45172.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.065250 restraints weight = 33250.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.065477 restraints weight = 31518.760| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18573 Z= 0.160 Angle : 0.607 7.577 25276 Z= 0.306 Chirality : 0.042 0.248 3068 Planarity : 0.004 0.055 3177 Dihedral : 7.491 63.173 2630 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 0.05 % Allowed : 3.33 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.18), residues: 2408 helix: 1.02 (0.18), residues: 974 sheet: -1.42 (0.29), residues: 321 loop : -1.69 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 772 TYR 0.014 0.001 TYR E1402 PHE 0.019 0.002 PHE E 671 TRP 0.031 0.002 TRP E2104 HIS 0.006 0.001 HIS E1584 Details of bonding type rmsd covalent geometry : bond 0.00363 (18573) covalent geometry : angle 0.60671 (25276) hydrogen bonds : bond 0.03215 ( 754) hydrogen bonds : angle 4.46750 ( 2136) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.660 Fit side-chains REVERT: B 87 MET cc_start: 0.4747 (tmm) cc_final: 0.4394 (tmm) REVERT: E 188 PHE cc_start: 0.8661 (m-80) cc_final: 0.8368 (m-10) REVERT: E 586 MET cc_start: 0.8447 (mmm) cc_final: 0.7960 (mmp) REVERT: E 1203 MET cc_start: 0.8762 (mmt) cc_final: 0.8304 (mmm) REVERT: E 1602 TRP cc_start: 0.7831 (t60) cc_final: 0.7548 (t-100) REVERT: E 2106 MET cc_start: 0.8955 (ppp) cc_final: 0.8434 (tmm) REVERT: E 2470 MET cc_start: 0.8056 (mmm) cc_final: 0.7825 (mmm) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.1099 time to fit residues: 25.1553 Evaluate side-chains 101 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 222 optimal weight: 0.0170 chunk 66 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 240 optimal weight: 9.9990 chunk 238 optimal weight: 0.8980 chunk 155 optimal weight: 0.5980 chunk 192 optimal weight: 0.5980 chunk 202 optimal weight: 3.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 301 GLN ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1101 ASN E2113 GLN ** E2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.084799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.065835 restraints weight = 80103.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.065369 restraints weight = 49257.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.066176 restraints weight = 42915.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.066494 restraints weight = 32677.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.066809 restraints weight = 31206.957| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18573 Z= 0.105 Angle : 0.563 7.078 25276 Z= 0.281 Chirality : 0.041 0.199 3068 Planarity : 0.003 0.052 3177 Dihedral : 7.225 62.873 2630 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.18), residues: 2408 helix: 1.15 (0.18), residues: 975 sheet: -1.32 (0.30), residues: 321 loop : -1.69 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E2176 TYR 0.013 0.001 TYR E1419 PHE 0.019 0.001 PHE E1047 TRP 0.027 0.001 TRP E2104 HIS 0.004 0.001 HIS E 408 Details of bonding type rmsd covalent geometry : bond 0.00237 (18573) covalent geometry : angle 0.56270 (25276) hydrogen bonds : bond 0.02873 ( 754) hydrogen bonds : angle 4.29501 ( 2136) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: B 28 SER cc_start: 0.7739 (t) cc_final: 0.7435 (p) REVERT: B 87 MET cc_start: 0.5146 (tmm) cc_final: 0.4833 (tmm) REVERT: B 144 LYS cc_start: 0.8087 (pttp) cc_final: 0.7886 (pttm) REVERT: E 188 PHE cc_start: 0.8635 (m-80) cc_final: 0.8366 (m-10) REVERT: E 586 MET cc_start: 0.8461 (mmm) cc_final: 0.7975 (mmp) REVERT: E 1203 MET cc_start: 0.8683 (mmt) cc_final: 0.8182 (mmm) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1070 time to fit residues: 24.9971 Evaluate side-chains 103 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 42 optimal weight: 0.0040 chunk 168 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 49 optimal weight: 0.4980 chunk 214 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 205 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 234 optimal weight: 0.6980 chunk 151 optimal weight: 5.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 230 HIS ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2453 ASN ** E2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.084976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.065853 restraints weight = 80357.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.065453 restraints weight = 53572.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.065992 restraints weight = 47039.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.066574 restraints weight = 35159.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.066708 restraints weight = 31804.241| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18573 Z= 0.104 Angle : 0.567 9.858 25276 Z= 0.282 Chirality : 0.041 0.208 3068 Planarity : 0.003 0.056 3177 Dihedral : 7.006 64.162 2630 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.18), residues: 2408 helix: 1.15 (0.18), residues: 981 sheet: -1.28 (0.30), residues: 321 loop : -1.68 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E2176 TYR 0.013 0.001 TYR B 77 PHE 0.013 0.001 PHE E1047 TRP 0.025 0.001 TRP E1602 HIS 0.004 0.001 HIS E1929 Details of bonding type rmsd covalent geometry : bond 0.00232 (18573) covalent geometry : angle 0.56715 (25276) hydrogen bonds : bond 0.02791 ( 754) hydrogen bonds : angle 4.22353 ( 2136) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.783 Fit side-chains REVERT: B 28 SER cc_start: 0.7813 (t) cc_final: 0.7526 (p) REVERT: B 144 LYS cc_start: 0.8022 (pttp) cc_final: 0.7784 (pttm) REVERT: E 188 PHE cc_start: 0.8614 (m-80) cc_final: 0.8298 (m-10) REVERT: E 449 MET cc_start: 0.8182 (mtm) cc_final: 0.7826 (mtm) REVERT: E 586 MET cc_start: 0.8430 (mmm) cc_final: 0.7996 (mmp) REVERT: E 1131 LEU cc_start: 0.8689 (mm) cc_final: 0.8451 (mm) REVERT: E 1203 MET cc_start: 0.8702 (mmt) cc_final: 0.8223 (mmm) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1150 time to fit residues: 26.7216 Evaluate side-chains 108 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 135 optimal weight: 0.0370 chunk 20 optimal weight: 50.0000 chunk 185 optimal weight: 3.9990 chunk 237 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 144 optimal weight: 0.0030 chunk 60 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.2070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 ASN ** E1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.083800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.064702 restraints weight = 79466.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.063549 restraints weight = 51134.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.064447 restraints weight = 47053.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.064654 restraints weight = 35665.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.064809 restraints weight = 34235.988| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18573 Z= 0.157 Angle : 0.608 8.500 25276 Z= 0.303 Chirality : 0.042 0.203 3068 Planarity : 0.004 0.055 3177 Dihedral : 6.912 62.981 2630 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 1.15 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.18), residues: 2408 helix: 1.13 (0.18), residues: 976 sheet: -1.33 (0.30), residues: 325 loop : -1.75 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E2176 TYR 0.011 0.001 TYR B 77 PHE 0.015 0.002 PHE E1883 TRP 0.031 0.002 TRP E1602 HIS 0.005 0.001 HIS E1043 Details of bonding type rmsd covalent geometry : bond 0.00361 (18573) covalent geometry : angle 0.60849 (25276) hydrogen bonds : bond 0.03023 ( 754) hydrogen bonds : angle 4.30579 ( 2136) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.689 Fit side-chains REVERT: B 144 LYS cc_start: 0.8029 (pttp) cc_final: 0.7779 (pttm) REVERT: E 188 PHE cc_start: 0.8691 (m-80) cc_final: 0.8397 (m-10) REVERT: E 449 MET cc_start: 0.8242 (mtm) cc_final: 0.7807 (mtm) REVERT: E 586 MET cc_start: 0.8498 (mmm) cc_final: 0.7944 (mmp) REVERT: E 1203 MET cc_start: 0.8726 (mmt) cc_final: 0.8354 (mmm) REVERT: E 2315 MET cc_start: 0.8057 (tpp) cc_final: 0.7753 (mmm) REVERT: E 2459 MET cc_start: 0.7646 (ppp) cc_final: 0.7422 (ppp) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1100 time to fit residues: 23.3244 Evaluate side-chains 104 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 217 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 240 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 234 optimal weight: 0.0980 chunk 197 optimal weight: 10.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 560 GLN E1093 ASN ** E1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.082231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.063111 restraints weight = 79693.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.062066 restraints weight = 52168.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.062935 restraints weight = 48022.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.063308 restraints weight = 35564.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.063485 restraints weight = 34400.475| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18573 Z= 0.219 Angle : 0.678 9.416 25276 Z= 0.339 Chirality : 0.044 0.195 3068 Planarity : 0.004 0.058 3177 Dihedral : 6.913 67.068 2630 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 1.15 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.18), residues: 2408 helix: 0.87 (0.17), residues: 986 sheet: -1.58 (0.29), residues: 327 loop : -1.79 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E2176 TYR 0.020 0.002 TYR E1402 PHE 0.020 0.002 PHE E1883 TRP 0.037 0.002 TRP E1602 HIS 0.007 0.001 HIS E1043 Details of bonding type rmsd covalent geometry : bond 0.00500 (18573) covalent geometry : angle 0.67828 (25276) hydrogen bonds : bond 0.03392 ( 754) hydrogen bonds : angle 4.54224 ( 2136) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.574 Fit side-chains REVERT: B 144 LYS cc_start: 0.8013 (pttp) cc_final: 0.7717 (pttm) REVERT: E 188 PHE cc_start: 0.8630 (m-80) cc_final: 0.8300 (m-10) REVERT: E 449 MET cc_start: 0.8249 (mtm) cc_final: 0.7832 (mtm) REVERT: E 586 MET cc_start: 0.8610 (mmm) cc_final: 0.7887 (mmp) REVERT: E 1131 LEU cc_start: 0.8872 (mm) cc_final: 0.8670 (mm) REVERT: E 1203 MET cc_start: 0.8820 (mmt) cc_final: 0.8433 (mmm) REVERT: E 1702 MET cc_start: 0.7805 (mmm) cc_final: 0.7408 (mmm) REVERT: E 2459 MET cc_start: 0.7729 (ppp) cc_final: 0.7414 (ppp) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1094 time to fit residues: 23.5698 Evaluate side-chains 105 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 200 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 235 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 204 optimal weight: 0.0170 chunk 185 optimal weight: 0.4980 chunk 23 optimal weight: 20.0000 chunk 232 optimal weight: 0.8980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1209 GLN ** E1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1783 HIS ** E2173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2510 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.084222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.065173 restraints weight = 78754.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.064647 restraints weight = 48478.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.065420 restraints weight = 43129.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.065836 restraints weight = 32926.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.066018 restraints weight = 31357.443| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18573 Z= 0.108 Angle : 0.595 9.937 25276 Z= 0.294 Chirality : 0.042 0.218 3068 Planarity : 0.003 0.056 3177 Dihedral : 6.557 67.171 2630 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 1.15 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.18), residues: 2408 helix: 1.03 (0.18), residues: 989 sheet: -1.46 (0.29), residues: 333 loop : -1.69 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E2176 TYR 0.013 0.001 TYR E1992 PHE 0.017 0.001 PHE E1047 TRP 0.034 0.001 TRP E1602 HIS 0.006 0.001 HIS E1783 Details of bonding type rmsd covalent geometry : bond 0.00245 (18573) covalent geometry : angle 0.59474 (25276) hydrogen bonds : bond 0.02928 ( 754) hydrogen bonds : angle 4.28708 ( 2136) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.705 Fit side-chains REVERT: E 1131 LEU cc_start: 0.8682 (mm) cc_final: 0.8444 (mm) REVERT: E 1203 MET cc_start: 0.8759 (mmt) cc_final: 0.8272 (mmm) REVERT: E 1259 GLU cc_start: 0.7768 (pp20) cc_final: 0.7544 (pp20) REVERT: E 1419 TYR cc_start: 0.7441 (m-10) cc_final: 0.7088 (m-10) REVERT: E 1702 MET cc_start: 0.7828 (mmm) cc_final: 0.7384 (mmm) REVERT: E 2459 MET cc_start: 0.7470 (ppp) cc_final: 0.7197 (ppp) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1090 time to fit residues: 24.9754 Evaluate side-chains 105 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 200 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 222 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 238 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.083699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.064824 restraints weight = 79882.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.063810 restraints weight = 50547.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.064658 restraints weight = 46259.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.065070 restraints weight = 34257.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.065438 restraints weight = 31823.570| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18573 Z= 0.129 Angle : 0.599 8.418 25276 Z= 0.297 Chirality : 0.042 0.188 3068 Planarity : 0.003 0.055 3177 Dihedral : 6.439 66.892 2630 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 1.15 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.18), residues: 2408 helix: 1.12 (0.18), residues: 977 sheet: -1.43 (0.29), residues: 333 loop : -1.72 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E2176 TYR 0.013 0.001 TYR E1402 PHE 0.019 0.001 PHE E1047 TRP 0.050 0.002 TRP E2104 HIS 0.004 0.001 HIS E1929 Details of bonding type rmsd covalent geometry : bond 0.00299 (18573) covalent geometry : angle 0.59931 (25276) hydrogen bonds : bond 0.02945 ( 754) hydrogen bonds : angle 4.29759 ( 2136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2609.74 seconds wall clock time: 46 minutes 19.13 seconds (2779.13 seconds total)