Starting phenix.real_space_refine on Thu Mar 5 03:26:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7orm_13042/03_2026/7orm_13042.cif Found real_map, /net/cci-nas-00/data/ceres_data/7orm_13042/03_2026/7orm_13042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7orm_13042/03_2026/7orm_13042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7orm_13042/03_2026/7orm_13042.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7orm_13042/03_2026/7orm_13042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7orm_13042/03_2026/7orm_13042.map" } resolution = 3.3 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= 0.002 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 40 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 11581 2.51 5 N 3077 2.21 5 O 3556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18369 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 299 Classifications: {'RNA': 14} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain: "T" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 231 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 10} Chain: "P" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 321 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 7, 'rna3p_pyr': 3} Link IDs: {'rna2p': 4, 'rna3p': 10} Chain: "A" Number of atoms: 17516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2145, 17516 Classifications: {'peptide': 2145} Link IDs: {'PTRANS': 70, 'TRANS': 2074} Chain breaks: 8 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16896 SG CYS A2064 61.779 37.228 30.093 1.00 92.99 S Time building chain proxies: 4.26, per 1000 atoms: 0.23 Number of scatterers: 18369 At special positions: 0 Unit cell: (106.485, 137.4, 139.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 113 16.00 P 40 15.00 Mg 1 11.99 O 3556 8.00 N 3077 7.00 C 11581 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: 1.56 Conformation dependent library (CDL) restraints added in 826.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" SG CYS A2064 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A2169 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A2182 " 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4136 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 17 sheets defined 56.7% alpha, 10.0% beta 10 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 2 through 16 Processing helix chain 'A' and resid 18 through 46 removed outlier: 3.956A pdb=" N LYS A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP A 24 " --> pdb=" O CYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 99 through 121 removed outlier: 4.446A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ILE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 149 removed outlier: 3.598A pdb=" N LYS A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 172 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 200 through 203 Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.540A pdb=" N MET A 214 " --> pdb=" O PHE A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 Processing helix chain 'A' and resid 237 through 262 removed outlier: 3.704A pdb=" N LYS A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASP A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 273 through 292 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 357 through 373 Processing helix chain 'A' and resid 407 through 417 Processing helix chain 'A' and resid 447 through 466 Processing helix chain 'A' and resid 475 through 489 removed outlier: 6.104A pdb=" N SER A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ARG A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 502 Processing helix chain 'A' and resid 502 through 523 removed outlier: 3.793A pdb=" N GLN A 506 " --> pdb=" O THR A 502 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 620 Proline residue: A 608 - end of helix Processing helix chain 'A' and resid 626 through 639 removed outlier: 3.690A pdb=" N TYR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 661 removed outlier: 3.983A pdb=" N LEU A 646 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Proline residue: A 651 - end of helix removed outlier: 4.055A pdb=" N TYR A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 673 Processing helix chain 'A' and resid 680 through 700 removed outlier: 3.600A pdb=" N PHE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 747 Processing helix chain 'A' and resid 748 through 752 Processing helix chain 'A' and resid 758 through 780 removed outlier: 4.157A pdb=" N VAL A 764 " --> pdb=" O HIS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 814 removed outlier: 3.580A pdb=" N HIS A 814 " --> pdb=" O ASP A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 830 through 838 removed outlier: 5.943A pdb=" N SER A 835 " --> pdb=" O THR A 832 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR A 836 " --> pdb=" O THR A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 854 Processing helix chain 'A' and resid 893 through 900 Processing helix chain 'A' and resid 911 through 921 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.572A pdb=" N GLN A 932 " --> pdb=" O PRO A 928 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 938 " --> pdb=" O MET A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 983 removed outlier: 3.807A pdb=" N ARG A 981 " --> pdb=" O ILE A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1020 Processing helix chain 'A' and resid 1020 through 1028 Processing helix chain 'A' and resid 1043 through 1049 Processing helix chain 'A' and resid 1070 through 1079 removed outlier: 4.011A pdb=" N PHE A1074 " --> pdb=" O PHE A1070 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TRP A1075 " --> pdb=" O TYR A1071 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A1076 " --> pdb=" O LYS A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1099 Processing helix chain 'A' and resid 1106 through 1115 removed outlier: 3.554A pdb=" N ASP A1115 " --> pdb=" O PHE A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1129 Processing helix chain 'A' and resid 1148 through 1174 Processing helix chain 'A' and resid 1201 through 1220 removed outlier: 3.886A pdb=" N ILE A1205 " --> pdb=" O GLU A1201 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1258 Processing helix chain 'A' and resid 1259 through 1261 No H-bonds generated for 'chain 'A' and resid 1259 through 1261' Processing helix chain 'A' and resid 1267 through 1285 removed outlier: 3.509A pdb=" N ASP A1271 " --> pdb=" O GLY A1267 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A1272 " --> pdb=" O PRO A1268 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER A1278 " --> pdb=" O SER A1274 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A1279 " --> pdb=" O ARG A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1307 Processing helix chain 'A' and resid 1317 through 1321 removed outlier: 3.852A pdb=" N PHE A1321 " --> pdb=" O ILE A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1334 Processing helix chain 'A' and resid 1340 through 1348 Processing helix chain 'A' and resid 1350 through 1365 Processing helix chain 'A' and resid 1373 through 1380 removed outlier: 3.690A pdb=" N GLU A1380 " --> pdb=" O ASN A1376 " (cutoff:3.500A) Processing helix chain 'A' and resid 1381 through 1384 Processing helix chain 'A' and resid 1390 through 1403 Processing helix chain 'A' and resid 1418 through 1422 removed outlier: 3.522A pdb=" N ARG A1422 " --> pdb=" O SER A1419 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1453 Processing helix chain 'A' and resid 1455 through 1467 removed outlier: 3.969A pdb=" N GLU A1459 " --> pdb=" O GLY A1455 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A1460 " --> pdb=" O GLY A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1472 removed outlier: 3.883A pdb=" N VAL A1472 " --> pdb=" O GLU A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1489 Processing helix chain 'A' and resid 1491 through 1499 Processing helix chain 'A' and resid 1502 through 1513 removed outlier: 3.555A pdb=" N LEU A1506 " --> pdb=" O ASN A1502 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1528 removed outlier: 4.048A pdb=" N TYR A1528 " --> pdb=" O ILE A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1548 through 1563 removed outlier: 3.952A pdb=" N SER A1562 " --> pdb=" O ARG A1558 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A1563 " --> pdb=" O ASP A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1578 Processing helix chain 'A' and resid 1581 through 1593 Processing helix chain 'A' and resid 1622 through 1632 removed outlier: 3.654A pdb=" N LYS A1632 " --> pdb=" O ARG A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1641 through 1660 Processing helix chain 'A' and resid 1660 through 1677 Processing helix chain 'A' and resid 1680 through 1700 Processing helix chain 'A' and resid 1717 through 1729 Processing helix chain 'A' and resid 1760 through 1779 Processing helix chain 'A' and resid 1783 through 1795 Processing helix chain 'A' and resid 1802 through 1811 Processing helix chain 'A' and resid 1818 through 1825 Processing helix chain 'A' and resid 1830 through 1841 Processing helix chain 'A' and resid 1892 through 1904 Processing helix chain 'A' and resid 1944 through 1954 Processing helix chain 'A' and resid 1983 through 1991 Processing helix chain 'A' and resid 2014 through 2019 removed outlier: 3.614A pdb=" N LYS A2017 " --> pdb=" O HIS A2014 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A2019 " --> pdb=" O SER A2016 " (cutoff:3.500A) Processing helix chain 'A' and resid 2033 through 2039 Processing helix chain 'A' and resid 2046 through 2052 removed outlier: 3.519A pdb=" N ILE A2050 " --> pdb=" O ASN A2046 " (cutoff:3.500A) Processing helix chain 'A' and resid 2054 through 2059 Processing helix chain 'A' and resid 2060 through 2062 No H-bonds generated for 'chain 'A' and resid 2060 through 2062' Processing helix chain 'A' and resid 2069 through 2075 removed outlier: 3.591A pdb=" N GLY A2073 " --> pdb=" O ASN A2069 " (cutoff:3.500A) Processing helix chain 'A' and resid 2109 through 2127 Processing helix chain 'A' and resid 2138 through 2155 Processing helix chain 'A' and resid 2158 through 2175 Processing helix chain 'A' and resid 2177 through 2183 Processing helix chain 'A' and resid 2200 through 2210 Processing helix chain 'A' and resid 2216 through 2238 removed outlier: 4.679A pdb=" N VAL A2221 " --> pdb=" O PRO A2217 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N MET A2222 " --> pdb=" O PRO A2218 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE A2238 " --> pdb=" O ILE A2234 " (cutoff:3.500A) Processing helix chain 'A' and resid 2246 through 2251 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.457A pdb=" N LEU A 88 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL A 127 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE A 90 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE A 129 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP A 92 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE A 131 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LYS A 94 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 295 Processing sheet with id=AA3, first strand: chain 'A' and resid 386 through 387 removed outlier: 6.975A pdb=" N VAL A 393 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N MET A 400 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP A 395 " --> pdb=" O GLN A 398 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE A 561 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 586 " --> pdb=" O CYS A 583 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 387 removed outlier: 6.975A pdb=" N VAL A 393 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N MET A 400 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP A 395 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 716 through 717 removed outlier: 6.586A pdb=" N ILE A 709 " --> pdb=" O TYR A2099 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N SER A2101 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N LEU A 711 " --> pdb=" O SER A2101 " (cutoff:3.500A) removed outlier: 11.602A pdb=" N ARG A2103 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 727 through 728 Processing sheet with id=AA7, first strand: chain 'A' and resid 842 through 846 Processing sheet with id=AA8, first strand: chain 'A' and resid 959 through 962 removed outlier: 6.259A pdb=" N PHE A 945 " --> pdb=" O ILE A1104 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A1101 " --> pdb=" O ILE A1139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1177 through 1184 removed outlier: 3.665A pdb=" N GLN A1197 " --> pdb=" O LYS A1051 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1236 through 1237 Processing sheet with id=AB2, first strand: chain 'A' and resid 1519 through 1520 Processing sheet with id=AB3, first strand: chain 'A' and resid 1594 through 1596 Processing sheet with id=AB4, first strand: chain 'A' and resid 1606 through 1609 Processing sheet with id=AB5, first strand: chain 'A' and resid 1800 through 1801 Processing sheet with id=AB6, first strand: chain 'A' and resid 1865 through 1867 removed outlier: 7.456A pdb=" N THR A1882 " --> pdb=" O VAL A1970 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ASN A1972 " --> pdb=" O THR A1882 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA A1884 " --> pdb=" O ASN A1972 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ALA A1974 " --> pdb=" O ALA A1884 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU A1886 " --> pdb=" O ALA A1974 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE A1927 " --> pdb=" O VAL A1968 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL A1970 " --> pdb=" O TYR A1925 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N TYR A1925 " --> pdb=" O VAL A1970 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A1940 " --> pdb=" O THR A1928 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG A1930 " --> pdb=" O VAL A1938 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A1938 " --> pdb=" O ARG A1930 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1999 through 2000 Processing sheet with id=AB8, first strand: chain 'A' and resid 2027 through 2028 918 hydrogen bonds defined for protein. 2640 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 4.56 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2942 1.30 - 1.43: 5094 1.43 - 1.56: 10520 1.56 - 1.69: 77 1.69 - 1.82: 187 Bond restraints: 18820 Sorted by residual: bond pdb=" C ASN A 826 " pdb=" O ASN A 826 " ideal model delta sigma weight residual 1.233 1.177 0.056 1.30e-02 5.92e+03 1.85e+01 bond pdb=" C PRO A1288 " pdb=" O PRO A1288 " ideal model delta sigma weight residual 1.243 1.209 0.035 8.50e-03 1.38e+04 1.66e+01 bond pdb=" N ILE A1730 " pdb=" CA ILE A1730 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.06e-02 8.90e+03 1.31e+01 bond pdb=" N ILE A1637 " pdb=" CA ILE A1637 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.11e-02 8.12e+03 1.14e+01 bond pdb=" CA SER A1192 " pdb=" CB SER A1192 " ideal model delta sigma weight residual 1.531 1.480 0.051 1.52e-02 4.33e+03 1.12e+01 ... (remaining 18815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 24536 1.69 - 3.37: 861 3.37 - 5.06: 136 5.06 - 6.75: 25 6.75 - 8.44: 6 Bond angle restraints: 25564 Sorted by residual: angle pdb=" N TYR A 714 " pdb=" CA TYR A 714 " pdb=" C TYR A 714 " ideal model delta sigma weight residual 113.97 105.53 8.44 1.28e+00 6.10e-01 4.34e+01 angle pdb=" CA ILE A1057 " pdb=" C ILE A1057 " pdb=" O ILE A1057 " ideal model delta sigma weight residual 122.63 117.67 4.96 8.70e-01 1.32e+00 3.25e+01 angle pdb=" CA ASN A 826 " pdb=" C ASN A 826 " pdb=" O ASN A 826 " ideal model delta sigma weight residual 121.65 115.25 6.40 1.17e+00 7.31e-01 2.99e+01 angle pdb=" N LEU A1828 " pdb=" CA LEU A1828 " pdb=" C LEU A1828 " ideal model delta sigma weight residual 112.93 105.73 7.20 1.33e+00 5.65e-01 2.93e+01 angle pdb=" N PRO A2217 " pdb=" CA PRO A2217 " pdb=" C PRO A2217 " ideal model delta sigma weight residual 110.70 117.24 -6.54 1.22e+00 6.72e-01 2.87e+01 ... (remaining 25559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 11235 34.69 - 69.39: 256 69.39 - 104.08: 22 104.08 - 138.77: 0 138.77 - 173.47: 1 Dihedral angle restraints: 11514 sinusoidal: 5146 harmonic: 6368 Sorted by residual: dihedral pdb=" O4' U P 7 " pdb=" C1' U P 7 " pdb=" N1 U P 7 " pdb=" C2 U P 7 " ideal model delta sinusoidal sigma weight residual -128.00 45.47 -173.47 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" C5' A P 8 " pdb=" C4' A P 8 " pdb=" C3' A P 8 " pdb=" O3' A P 8 " ideal model delta sinusoidal sigma weight residual 147.00 112.47 34.53 1 8.00e+00 1.56e-02 2.64e+01 dihedral pdb=" CA TRP A1143 " pdb=" C TRP A1143 " pdb=" N LEU A1144 " pdb=" CA LEU A1144 " ideal model delta harmonic sigma weight residual 180.00 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 11511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2410 0.059 - 0.117: 370 0.117 - 0.176: 66 0.176 - 0.234: 26 0.234 - 0.293: 5 Chirality restraints: 2877 Sorted by residual: chirality pdb=" CA ASP A 35 " pdb=" N ASP A 35 " pdb=" C ASP A 35 " pdb=" CB ASP A 35 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA ILE A1637 " pdb=" N ILE A1637 " pdb=" C ILE A1637 " pdb=" CB ILE A1637 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CB ILE A1706 " pdb=" CA ILE A1706 " pdb=" CG1 ILE A1706 " pdb=" CG2 ILE A1706 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 2874 not shown) Planarity restraints: 3093 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A1368 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.97e+00 pdb=" C MET A1368 " -0.052 2.00e-02 2.50e+03 pdb=" O MET A1368 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN A1369 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1826 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.79e+00 pdb=" C GLY A1826 " -0.048 2.00e-02 2.50e+03 pdb=" O GLY A1826 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP A1827 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A2118 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" C ILE A2118 " -0.046 2.00e-02 2.50e+03 pdb=" O ILE A2118 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU A2119 " 0.016 2.00e-02 2.50e+03 ... (remaining 3090 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 81 2.58 - 3.16: 15299 3.16 - 3.74: 28822 3.74 - 4.32: 40977 4.32 - 4.90: 67783 Nonbonded interactions: 152962 Sorted by model distance: nonbonded pdb=" OD1 ASP A2178 " pdb="ZN ZN A2301 " model vdw 2.004 2.230 nonbonded pdb=" OD1 ASP A1188 " pdb="MG MG A2302 " model vdw 2.041 2.170 nonbonded pdb=" OG SER A1443 " pdb=" OH TYR A1489 " model vdw 2.291 3.040 nonbonded pdb=" O ILE A1875 " pdb=" OG1 THR A1882 " model vdw 2.335 3.040 nonbonded pdb=" OD1 ASN A1924 " pdb=" OH TYR A1926 " model vdw 2.366 3.040 ... (remaining 152957 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.540 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 : 0.005 0.197 18823 Z= 0.299 Angle : 0.705 8.437 25564 Z= 0.478 Chirality : 0.049 0.293 2877 Planarity : 0.004 0.043 3093 Dihedral : 14.428 173.466 7378 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.76 % Rotamer: Outliers : 0.20 % Allowed : 1.51 % Favored : 98.28 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.18), residues: 2127 helix: 1.72 (0.16), residues: 1109 sheet: 0.31 (0.43), residues: 149 loop : -1.15 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2205 TYR 0.013 0.001 TYR A1463 PHE 0.032 0.001 PHE A 511 TRP 0.026 0.001 TRP A2160 HIS 0.003 0.001 HIS A1749 Details of bonding type rmsd covalent geometry : bond 0.00430 (18820) covalent geometry : angle 0.70462 (25564) hydrogen bonds : bond 0.14769 ( 928) hydrogen bonds : angle 5.86054 ( 2686) metal coordination : bond 0.12567 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 228 time to evaluate : 0.579 Fit side-chains REVERT: A 417 ASN cc_start: 0.8351 (m-40) cc_final: 0.8058 (m-40) REVERT: A 553 LYS cc_start: 0.8088 (mptt) cc_final: 0.7655 (mttp) REVERT: A 714 TYR cc_start: 0.6397 (m-80) cc_final: 0.6164 (m-80) REVERT: A 1430 ARG cc_start: 0.7832 (tpp80) cc_final: 0.7528 (mmt-90) REVERT: A 2160 TRP cc_start: 0.7619 (m-10) cc_final: 0.7194 (m-10) outliers start: 4 outliers final: 3 residues processed: 232 average time/residue: 0.1448 time to fit residues: 51.2773 Evaluate side-chains 171 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 168 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1278 SER Chi-restraints excluded: chain A residue 1825 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN A 757 HIS A 823 ASN A 952 GLN A1007 GLN A1116 GLN A1223 GLN A1334 ASN ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.125872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.088866 restraints weight = 28126.218| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.97 r_work: 0.2886 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18823 Z= 0.149 Angle : 0.522 8.172 25564 Z= 0.281 Chirality : 0.041 0.161 2877 Planarity : 0.004 0.045 3093 Dihedral : 12.227 170.760 2929 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.66 % Allowed : 5.91 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.18), residues: 2127 helix: 1.94 (0.15), residues: 1129 sheet: 0.92 (0.41), residues: 156 loop : -1.26 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1628 TYR 0.013 0.001 TYR A 750 PHE 0.024 0.001 PHE A 511 TRP 0.010 0.001 TRP A1075 HIS 0.008 0.001 HIS A2169 Details of bonding type rmsd covalent geometry : bond 0.00336 (18820) covalent geometry : angle 0.52214 (25564) hydrogen bonds : bond 0.04487 ( 928) hydrogen bonds : angle 4.53112 ( 2686) metal coordination : bond 0.00185 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 185 time to evaluate : 0.690 Fit side-chains REVERT: A 417 ASN cc_start: 0.8565 (m-40) cc_final: 0.8151 (m-40) REVERT: A 553 LYS cc_start: 0.8089 (mptt) cc_final: 0.7472 (mttp) REVERT: A 825 ASN cc_start: 0.8849 (m110) cc_final: 0.8440 (m-40) REVERT: A 1406 ASP cc_start: 0.8163 (m-30) cc_final: 0.7913 (m-30) REVERT: A 1430 ARG cc_start: 0.8306 (tpp80) cc_final: 0.7849 (mmt-90) REVERT: A 2038 LYS cc_start: 0.9157 (mtmt) cc_final: 0.8849 (mtpt) REVERT: A 2082 MET cc_start: 0.8425 (mtt) cc_final: 0.8185 (mtt) REVERT: A 2160 TRP cc_start: 0.7783 (m-10) cc_final: 0.7418 (m-10) REVERT: A 2180 MET cc_start: 0.7420 (tpt) cc_final: 0.7069 (tpt) outliers start: 13 outliers final: 8 residues processed: 190 average time/residue: 0.1489 time to fit residues: 43.1219 Evaluate side-chains 172 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1278 SER Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1825 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 204 optimal weight: 0.7980 chunk 185 optimal weight: 9.9990 chunk 60 optimal weight: 0.4980 chunk 24 optimal weight: 0.2980 chunk 104 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1112 ASN ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2169 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 = 0.3581 r_free = 0.3581 target = 0.126778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.089865 restraints weight = 28066.567| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.97 r_work: 0.2905 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18823 Z= 0.115 Angle : 0.479 7.352 25564 Z= 0.257 Chirality : 0.040 0.161 2877 Planarity : 0.003 0.048 3093 Dihedral : 12.178 171.351 2926 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.96 % Allowed : 7.42 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.09 (0.18), residues: 2127 helix: 2.01 (0.15), residues: 1129 sheet: 1.10 (0.42), residues: 156 loop : -1.20 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 235 TYR 0.012 0.001 TYR A1463 PHE 0.017 0.001 PHE A 511 TRP 0.010 0.001 TRP A1143 HIS 0.007 0.001 HIS A2169 Details of bonding type rmsd covalent geometry : bond 0.00257 (18820) covalent geometry : angle 0.47927 (25564) hydrogen bonds : bond 0.03758 ( 928) hydrogen bonds : angle 4.25536 ( 2686) metal coordination : bond 0.00067 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.700 Fit side-chains REVERT: A 417 ASN cc_start: 0.8489 (m-40) cc_final: 0.8187 (m-40) REVERT: A 553 LYS cc_start: 0.8060 (mptt) cc_final: 0.7441 (mttp) REVERT: A 788 ASN cc_start: 0.8790 (p0) cc_final: 0.8418 (p0) REVERT: A 825 ASN cc_start: 0.8758 (m110) cc_final: 0.8379 (m-40) REVERT: A 960 ILE cc_start: 0.8424 (mm) cc_final: 0.7991 (mm) REVERT: A 1173 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8142 (mp) REVERT: A 1430 ARG cc_start: 0.8298 (tpp80) cc_final: 0.7829 (mmt-90) REVERT: A 1574 TYR cc_start: 0.8950 (m-80) cc_final: 0.8729 (m-80) REVERT: A 1661 LEU cc_start: 0.8610 (mt) cc_final: 0.8381 (mt) REVERT: A 2038 LYS cc_start: 0.9148 (mtmt) cc_final: 0.8880 (mtpt) REVERT: A 2160 TRP cc_start: 0.7888 (m-10) cc_final: 0.7523 (m-10) REVERT: A 2180 MET cc_start: 0.7618 (tpt) cc_final: 0.7231 (tpt) outliers start: 19 outliers final: 9 residues processed: 196 average time/residue: 0.1382 time to fit residues: 42.2756 Evaluate side-chains 178 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 168 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1278 SER Chi-restraints excluded: chain A residue 1671 MET Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1825 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 7 optimal weight: 0.5980 chunk 151 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 176 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 208 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 HIS A1112 ASN ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2169 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 = 0.3576 r_free = 0.3576 target = 0.126014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.088306 restraints weight = 28318.757| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.08 r_work: 0.2878 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18823 Z= 0.154 Angle : 0.499 7.937 25564 Z= 0.266 Chirality : 0.041 0.187 2877 Planarity : 0.004 0.050 3093 Dihedral : 12.139 171.608 2926 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.01 % Allowed : 8.68 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.10 (0.18), residues: 2127 helix: 2.01 (0.15), residues: 1127 sheet: 1.08 (0.41), residues: 156 loop : -1.19 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 235 TYR 0.013 0.001 TYR A 750 PHE 0.019 0.001 PHE A1768 TRP 0.009 0.001 TRP A1143 HIS 0.006 0.001 HIS A2169 Details of bonding type rmsd covalent geometry : bond 0.00363 (18820) covalent geometry : angle 0.49907 (25564) hydrogen bonds : bond 0.03948 ( 928) hydrogen bonds : angle 4.24564 ( 2686) metal coordination : bond 0.00278 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.449 Fit side-chains REVERT: A 417 ASN cc_start: 0.8465 (m-40) cc_final: 0.8205 (m-40) REVERT: A 553 LYS cc_start: 0.8044 (mptt) cc_final: 0.7416 (mttp) REVERT: A 788 ASN cc_start: 0.8814 (p0) cc_final: 0.8457 (p0) REVERT: A 825 ASN cc_start: 0.8842 (m110) cc_final: 0.8440 (m-40) REVERT: A 960 ILE cc_start: 0.8608 (mm) cc_final: 0.8164 (mm) REVERT: A 975 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8016 (mt-10) REVERT: A 1309 MET cc_start: 0.9140 (mmm) cc_final: 0.8829 (mtt) REVERT: A 1430 ARG cc_start: 0.8376 (tpp80) cc_final: 0.7939 (mmt-90) REVERT: A 1661 LEU cc_start: 0.8693 (mt) cc_final: 0.8368 (mt) REVERT: A 2160 TRP cc_start: 0.7852 (m-10) cc_final: 0.7465 (m-10) outliers start: 20 outliers final: 11 residues processed: 184 average time/residue: 0.1431 time to fit residues: 40.9889 Evaluate side-chains 174 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 1277 SER Chi-restraints excluded: chain A residue 1671 MET Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1927 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 13 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 193 optimal weight: 0.0010 chunk 93 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 207 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 125 optimal weight: 0.0010 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2141 ASN ** 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 = 0.3599 r_free = 0.3599 target = 0.127684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.090291 restraints weight = 27967.541| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.08 r_work: 0.2914 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 18823 Z= 0.103 Angle : 0.467 7.571 25564 Z= 0.249 Chirality : 0.039 0.157 2877 Planarity : 0.003 0.048 3093 Dihedral : 12.079 172.218 2925 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.96 % Allowed : 9.09 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.18), residues: 2127 helix: 2.10 (0.16), residues: 1130 sheet: 1.12 (0.41), residues: 156 loop : -1.14 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 119 TYR 0.012 0.001 TYR A1463 PHE 0.018 0.001 PHE A1768 TRP 0.010 0.001 TRP A1143 HIS 0.004 0.001 HIS A2169 Details of bonding type rmsd covalent geometry : bond 0.00230 (18820) covalent geometry : angle 0.46655 (25564) hydrogen bonds : bond 0.03487 ( 928) hydrogen bonds : angle 4.09104 ( 2686) metal coordination : bond 0.00068 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.686 Fit side-chains REVERT: A 417 ASN cc_start: 0.8513 (m-40) cc_final: 0.8271 (m-40) REVERT: A 553 LYS cc_start: 0.7985 (mptt) cc_final: 0.7420 (mttp) REVERT: A 763 MET cc_start: 0.9133 (mmm) cc_final: 0.8897 (mmp) REVERT: A 788 ASN cc_start: 0.8757 (p0) cc_final: 0.8361 (p0) REVERT: A 825 ASN cc_start: 0.8727 (m110) cc_final: 0.8360 (m-40) REVERT: A 975 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7959 (mt-10) REVERT: A 1309 MET cc_start: 0.9166 (mmm) cc_final: 0.8810 (mtp) REVERT: A 1430 ARG cc_start: 0.8374 (tpp80) cc_final: 0.7939 (mmt-90) REVERT: A 1661 LEU cc_start: 0.8641 (mt) cc_final: 0.8301 (mt) REVERT: A 2160 TRP cc_start: 0.7808 (m-10) cc_final: 0.7409 (m-10) outliers start: 19 outliers final: 13 residues processed: 187 average time/residue: 0.1369 time to fit residues: 40.5860 Evaluate side-chains 181 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1277 SER Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 2002 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 18 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 148 optimal weight: 0.0670 chunk 91 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 chunk 193 optimal weight: 0.1980 chunk 60 optimal weight: 4.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A1392 ASN ** A2141 ASN ** 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 = 0.3621 r_free = 0.3621 target = 0.129258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.092058 restraints weight = 27813.131| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.07 r_work: 0.2940 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18823 Z= 0.092 Angle : 0.455 9.059 25564 Z= 0.241 Chirality : 0.039 0.152 2877 Planarity : 0.003 0.047 3093 Dihedral : 11.997 172.952 2925 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.01 % Allowed : 9.59 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.30 (0.18), residues: 2127 helix: 2.18 (0.16), residues: 1133 sheet: 1.22 (0.42), residues: 151 loop : -1.11 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 119 TYR 0.013 0.001 TYR A1463 PHE 0.016 0.001 PHE A1768 TRP 0.011 0.001 TRP A1143 HIS 0.004 0.000 HIS A2169 Details of bonding type rmsd covalent geometry : bond 0.00201 (18820) covalent geometry : angle 0.45509 (25564) hydrogen bonds : bond 0.03212 ( 928) hydrogen bonds : angle 3.94806 ( 2686) metal coordination : bond 0.00090 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.600 Fit side-chains REVERT: A 417 ASN cc_start: 0.8452 (m-40) cc_final: 0.8233 (m-40) REVERT: A 553 LYS cc_start: 0.8064 (mptt) cc_final: 0.7457 (mttp) REVERT: A 763 MET cc_start: 0.8848 (mmm) cc_final: 0.8621 (mmt) REVERT: A 788 ASN cc_start: 0.8699 (p0) cc_final: 0.8302 (p0) REVERT: A 825 ASN cc_start: 0.8681 (m110) cc_final: 0.8300 (m-40) REVERT: A 959 GLU cc_start: 0.8292 (pm20) cc_final: 0.8044 (pm20) REVERT: A 975 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7986 (mt-10) REVERT: A 1128 MET cc_start: 0.8870 (mmm) cc_final: 0.8667 (mmm) REVERT: A 1309 MET cc_start: 0.9177 (mmm) cc_final: 0.8889 (mtt) REVERT: A 1420 ASP cc_start: 0.8731 (m-30) cc_final: 0.8529 (m-30) REVERT: A 1430 ARG cc_start: 0.8349 (tpp80) cc_final: 0.7975 (mmt-90) REVERT: A 1661 LEU cc_start: 0.8628 (mt) cc_final: 0.8323 (mt) REVERT: A 2160 TRP cc_start: 0.7723 (m-10) cc_final: 0.7224 (m-10) outliers start: 20 outliers final: 13 residues processed: 202 average time/residue: 0.1374 time to fit residues: 43.3654 Evaluate side-chains 184 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1277 SER Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 2002 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 138 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 152 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 GLN ** A2141 ASN ** 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 = 0.3552 r_free = 0.3552 target = 0.124288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.086427 restraints weight = 28166.870| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.07 r_work: 0.2843 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 18823 Z= 0.220 Angle : 0.553 10.374 25564 Z= 0.291 Chirality : 0.043 0.222 2877 Planarity : 0.004 0.048 3093 Dihedral : 12.024 171.375 2925 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.31 % Allowed : 10.40 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.18), residues: 2127 helix: 1.97 (0.16), residues: 1131 sheet: 1.02 (0.42), residues: 151 loop : -1.21 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 12 TYR 0.024 0.002 TYR A1320 PHE 0.021 0.002 PHE A1768 TRP 0.008 0.001 TRP A 395 HIS 0.005 0.001 HIS A1591 Details of bonding type rmsd covalent geometry : bond 0.00525 (18820) covalent geometry : angle 0.55306 (25564) hydrogen bonds : bond 0.04276 ( 928) hydrogen bonds : angle 4.23287 ( 2686) metal coordination : bond 0.00415 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.728 Fit side-chains REVERT: A 417 ASN cc_start: 0.8525 (m-40) cc_final: 0.8290 (m-40) REVERT: A 553 LYS cc_start: 0.7950 (mptt) cc_final: 0.7407 (mttp) REVERT: A 788 ASN cc_start: 0.8773 (p0) cc_final: 0.8391 (p0) REVERT: A 825 ASN cc_start: 0.8965 (m110) cc_final: 0.8538 (m-40) REVERT: A 1309 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.9059 (mtp) REVERT: A 1430 ARG cc_start: 0.8354 (tpp80) cc_final: 0.7924 (mmt-90) REVERT: A 2038 LYS cc_start: 0.9225 (mtmt) cc_final: 0.8968 (mtpt) REVERT: A 2160 TRP cc_start: 0.7720 (m-10) cc_final: 0.7262 (m-10) outliers start: 26 outliers final: 19 residues processed: 188 average time/residue: 0.1450 time to fit residues: 41.6237 Evaluate side-chains 183 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1067 GLN Chi-restraints excluded: chain A residue 1277 SER Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1706 ILE Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2093 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 180 optimal weight: 0.0970 chunk 36 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 164 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 167 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 GLN ** A2141 ASN ** 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 = 0.3583 r_free = 0.3583 target = 0.126613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.088976 restraints weight = 27901.799| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.08 r_work: 0.2889 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18823 Z= 0.123 Angle : 0.497 10.294 25564 Z= 0.261 Chirality : 0.040 0.211 2877 Planarity : 0.003 0.048 3093 Dihedral : 12.020 170.918 2925 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.26 % Allowed : 10.75 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.18), residues: 2127 helix: 2.07 (0.16), residues: 1128 sheet: 1.05 (0.42), residues: 151 loop : -1.18 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 235 TYR 0.016 0.001 TYR A1320 PHE 0.019 0.001 PHE A1768 TRP 0.010 0.001 TRP A1143 HIS 0.004 0.001 HIS A2169 Details of bonding type rmsd covalent geometry : bond 0.00282 (18820) covalent geometry : angle 0.49691 (25564) hydrogen bonds : bond 0.03642 ( 928) hydrogen bonds : angle 4.06476 ( 2686) metal coordination : bond 0.00124 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.684 Fit side-chains REVERT: A 417 ASN cc_start: 0.8392 (m-40) cc_final: 0.8151 (m-40) REVERT: A 553 LYS cc_start: 0.7964 (mptt) cc_final: 0.7424 (mttp) REVERT: A 825 ASN cc_start: 0.8790 (m110) cc_final: 0.8385 (m-40) REVERT: A 1309 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8970 (mtp) REVERT: A 1430 ARG cc_start: 0.8355 (tpp80) cc_final: 0.7924 (mmt-90) REVERT: A 2038 LYS cc_start: 0.9251 (mtmt) cc_final: 0.9004 (mtpt) REVERT: A 2082 MET cc_start: 0.8401 (mtt) cc_final: 0.8199 (mtt) REVERT: A 2160 TRP cc_start: 0.7750 (m-10) cc_final: 0.7273 (m-10) outliers start: 25 outliers final: 19 residues processed: 183 average time/residue: 0.1330 time to fit residues: 38.2608 Evaluate side-chains 187 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1067 GLN Chi-restraints excluded: chain A residue 1277 SER Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1671 MET Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1704 HIS Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 2002 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 107 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 GLN ** A2141 ASN ** 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 = 0.3573 r_free = 0.3573 target = 0.125922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.088284 restraints weight = 27934.941| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.07 r_work: 0.2875 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18823 Z= 0.144 Angle : 0.508 10.704 25564 Z= 0.267 Chirality : 0.040 0.203 2877 Planarity : 0.004 0.048 3093 Dihedral : 12.002 170.588 2925 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.26 % Allowed : 10.75 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.12 (0.18), residues: 2127 helix: 2.06 (0.15), residues: 1130 sheet: 1.03 (0.42), residues: 151 loop : -1.20 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2103 TYR 0.018 0.001 TYR A1320 PHE 0.026 0.001 PHE A 363 TRP 0.007 0.001 TRP A1143 HIS 0.004 0.001 HIS A2169 Details of bonding type rmsd covalent geometry : bond 0.00339 (18820) covalent geometry : angle 0.50836 (25564) hydrogen bonds : bond 0.03788 ( 928) hydrogen bonds : angle 4.08659 ( 2686) metal coordination : bond 0.00191 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.699 Fit side-chains REVERT: A 417 ASN cc_start: 0.8398 (m-40) cc_final: 0.8161 (m-40) REVERT: A 553 LYS cc_start: 0.7952 (mptt) cc_final: 0.7411 (mttp) REVERT: A 763 MET cc_start: 0.8843 (mmm) cc_final: 0.8573 (mmt) REVERT: A 825 ASN cc_start: 0.8842 (m110) cc_final: 0.8444 (m-40) REVERT: A 1309 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.9013 (mtp) REVERT: A 1430 ARG cc_start: 0.8370 (tpp80) cc_final: 0.7937 (mmt-90) REVERT: A 2038 LYS cc_start: 0.9267 (mtmt) cc_final: 0.9026 (mtpt) REVERT: A 2160 TRP cc_start: 0.7637 (m-10) cc_final: 0.7157 (m-10) outliers start: 25 outliers final: 21 residues processed: 181 average time/residue: 0.1447 time to fit residues: 40.4181 Evaluate side-chains 185 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1067 GLN Chi-restraints excluded: chain A residue 1277 SER Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1671 MET Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1704 HIS Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 2002 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 61 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 40 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 chunk 185 optimal weight: 30.0000 chunk 210 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 196 optimal weight: 0.9990 chunk 151 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 GLN ** A2141 ASN ** 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 = 0.3578 r_free = 0.3578 target = 0.126283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.088968 restraints weight = 27897.729| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.06 r_work: 0.2889 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18823 Z= 0.120 Angle : 0.494 10.749 25564 Z= 0.260 Chirality : 0.040 0.197 2877 Planarity : 0.003 0.048 3093 Dihedral : 11.993 170.624 2925 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.11 % Allowed : 11.00 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.18), residues: 2127 helix: 2.10 (0.15), residues: 1131 sheet: 1.04 (0.42), residues: 151 loop : -1.17 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2103 TYR 0.015 0.001 TYR A1320 PHE 0.029 0.001 PHE A 363 TRP 0.008 0.001 TRP A1143 HIS 0.004 0.001 HIS A2169 Details of bonding type rmsd covalent geometry : bond 0.00275 (18820) covalent geometry : angle 0.49434 (25564) hydrogen bonds : bond 0.03594 ( 928) hydrogen bonds : angle 4.02858 ( 2686) metal coordination : bond 0.00117 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.941 Fit side-chains REVERT: A 417 ASN cc_start: 0.8390 (m-40) cc_final: 0.8157 (m-40) REVERT: A 553 LYS cc_start: 0.7959 (mptt) cc_final: 0.7417 (mttp) REVERT: A 763 MET cc_start: 0.8794 (mmm) cc_final: 0.8537 (mmt) REVERT: A 825 ASN cc_start: 0.8782 (m110) cc_final: 0.8396 (m-40) REVERT: A 959 GLU cc_start: 0.8339 (pm20) cc_final: 0.8091 (pm20) REVERT: A 1128 MET cc_start: 0.8881 (mmm) cc_final: 0.8679 (mmm) REVERT: A 1309 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8961 (mtp) REVERT: A 1430 ARG cc_start: 0.8354 (tpp80) cc_final: 0.7938 (mmt-90) REVERT: A 2160 TRP cc_start: 0.7662 (m-10) cc_final: 0.7162 (m-10) outliers start: 22 outliers final: 19 residues processed: 184 average time/residue: 0.1365 time to fit residues: 38.8042 Evaluate side-chains 187 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1067 GLN Chi-restraints excluded: chain A residue 1277 SER Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1671 MET Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1704 HIS Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 2002 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 153 optimal weight: 0.3980 chunk 196 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 202 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 66 optimal weight: 0.0050 chunk 59 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 188 optimal weight: 10.0000 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 GLN ** A2141 ASN ** 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 = 0.3597 r_free = 0.3597 target = 0.127672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.090377 restraints weight = 27939.121| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.06 r_work: 0.2913 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18823 Z= 0.103 Angle : 0.484 10.799 25564 Z= 0.254 Chirality : 0.039 0.188 2877 Planarity : 0.003 0.048 3093 Dihedral : 11.957 171.090 2924 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.01 % Allowed : 11.36 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.24 (0.18), residues: 2127 helix: 2.15 (0.16), residues: 1131 sheet: 1.08 (0.42), residues: 151 loop : -1.14 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2103 TYR 0.014 0.001 TYR A1463 PHE 0.028 0.001 PHE A 363 TRP 0.010 0.001 TRP A1143 HIS 0.004 0.001 HIS A2169 Details of bonding type rmsd covalent geometry : bond 0.00229 (18820) covalent geometry : angle 0.48390 (25564) hydrogen bonds : bond 0.03377 ( 928) hydrogen bonds : angle 3.96065 ( 2686) metal coordination : bond 0.00061 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4548.74 seconds wall clock time: 79 minutes 1.31 seconds (4741.31 seconds total)