Starting phenix.real_space_refine on Thu Sep 18 13:49:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y2o_38859/09_2025/8y2o_38859.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y2o_38859/09_2025/8y2o_38859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y2o_38859/09_2025/8y2o_38859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y2o_38859/09_2025/8y2o_38859.map" model { file = "/net/cci-nas-00/data/ceres_data/8y2o_38859/09_2025/8y2o_38859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y2o_38859/09_2025/8y2o_38859.cif" } resolution = 2.66 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= 0.004 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 72 5.49 5 Mg 7 5.21 5 S 113 5.16 5 C 10816 2.51 5 N 2944 2.21 5 O 3432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17385 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 14101 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1786, 14093 Classifications: {'peptide': 1786} Link IDs: {'PTRANS': 73, 'TRANS': 1712} Chain breaks: 10 Conformer: "B" Number of residues, atoms: 1786, 14093 Classifications: {'peptide': 1786} Link IDs: {'PTRANS': 73, 'TRANS': 1712} Chain breaks: 10 bond proxies already assigned to first conformer: 14371 Chain: "B" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1708 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain breaks: 1 Chain: "C" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1542 Classifications: {'RNA': 72} Modifications used: {'p5*END': 1, 'rna2p_pur': 13, 'rna2p_pyr': 3, 'rna3p_pur': 26, 'rna3p_pyr': 30} Link IDs: {'rna2p': 16, 'rna3p': 55} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2151 SG CYS A 283 79.372 24.451 37.763 1.00 94.52 S ATOM 2275 SG CYS A 299 76.391 23.836 38.733 1.00 84.78 S Time building chain proxies: 5.87, per 1000 atoms: 0.34 Number of scatterers: 17385 At special positions: 0 Unit cell: (115.37, 139.44, 126.16, 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 72 15.00 Mg 7 11.99 O 3432 8.00 N 2944 7.00 C 10816 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: 1.29 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 283 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 299 " 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3844 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 2 sheets defined 75.1% alpha, 1.9% beta 26 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 19 through 26 removed outlier: 3.840A pdb=" N THR A 23 " --> pdb=" O GLN A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.806A pdb=" N LEU A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 64 removed outlier: 4.186A pdb=" N VAL A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix Processing helix chain 'A' and resid 72 through 88 Processing helix chain 'A' and resid 93 through 104 removed outlier: 4.101A pdb=" N LYS A 97 " --> pdb=" O ASN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 106 No H-bonds generated for 'chain 'A' and resid 105 through 106' Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 110 through 127 removed outlier: 3.537A pdb=" N ASN A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 148 through 158 removed outlier: 3.885A pdb=" N ALA A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 180 Processing helix chain 'A' and resid 183 through 207 removed outlier: 3.502A pdb=" N GLN A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 240 Processing helix chain 'A' and resid 244 through 263 Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 268 through 279 Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 320 through 324 removed outlier: 3.811A pdb=" N GLY A 323 " --> pdb=" O TRP A 320 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 324 " --> pdb=" O GLN A 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 320 through 324' Processing helix chain 'A' and resid 325 through 347 removed outlier: 3.739A pdb=" N SER A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 372 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.628A pdb=" N ASP A 380 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 400 Processing helix chain 'A' and resid 404 through 426 Processing helix chain 'A' and resid 434 through 445 Processing helix chain 'A' and resid 451 through 466 removed outlier: 4.100A pdb=" N TYR A 455 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 474 removed outlier: 4.171A pdb=" N ILE A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.658A pdb=" N VAL A 484 " --> pdb=" O GLN A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 490 through 510 Processing helix chain 'A' and resid 517 through 527 removed outlier: 4.006A pdb=" N GLN A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 537 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 549 through 557 Processing helix chain 'A' and resid 559 through 579 removed outlier: 4.075A pdb=" N TYR A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 570 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 576 " --> pdb=" O ILE A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 592 Processing helix chain 'A' and resid 592 through 607 Processing helix chain 'A' and resid 622 through 631 removed outlier: 3.573A pdb=" N ILE A 631 " --> pdb=" O LYS A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 647 Processing helix chain 'A' and resid 656 through 670 removed outlier: 3.923A pdb=" N TYR A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 705 removed outlier: 3.625A pdb=" N GLN A 698 " --> pdb=" O GLN A 694 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 699 " --> pdb=" O GLU A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 742 Processing helix chain 'A' and resid 748 through 766 Processing helix chain 'A' and resid 778 through 783 Processing helix chain 'A' and resid 784 through 794 Processing helix chain 'A' and resid 795 through 797 No H-bonds generated for 'chain 'A' and resid 795 through 797' Processing helix chain 'A' and resid 799 through 813 Processing helix chain 'A' and resid 822 through 837 Processing helix chain 'A' and resid 843 through 857 removed outlier: 3.892A pdb=" N THR A 847 " --> pdb=" O TYR A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 868 Processing helix chain 'A' and resid 880 through 910 Processing helix chain 'A' and resid 910 through 917 removed outlier: 3.850A pdb=" N ALA A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 934 removed outlier: 3.660A pdb=" N VAL A 924 " --> pdb=" O MET A 920 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 939 removed outlier: 3.834A pdb=" N LEU A 939 " --> pdb=" O LEU A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 969 Proline residue: A 947 - end of helix Proline residue: A 965 - end of helix Processing helix chain 'A' and resid 1045 through 1068 removed outlier: 3.563A pdb=" N VAL A1049 " --> pdb=" O THR A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1071 No H-bonds generated for 'chain 'A' and resid 1069 through 1071' Processing helix chain 'A' and resid 1085 through 1099 Processing helix chain 'A' and resid 1109 through 1126 removed outlier: 3.547A pdb=" N TYR A1113 " --> pdb=" O PHE A1109 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR A1114 " --> pdb=" O GLU A1110 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY A1115 " --> pdb=" O LEU A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1133 Processing helix chain 'A' and resid 1133 through 1148 removed outlier: 3.998A pdb=" N CYS A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1174 removed outlier: 3.570A pdb=" N SER A1174 " --> pdb=" O ALA A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1196 Processing helix chain 'A' and resid 1203 through 1220 removed outlier: 3.564A pdb=" N LEU A1211 " --> pdb=" O GLN A1207 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A1216 " --> pdb=" O ASN A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1223 through 1229 removed outlier: 3.629A pdb=" N ILE A1227 " --> pdb=" O GLY A1224 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A1228 " --> pdb=" O GLU A1225 " (cutoff:3.500A) Proline residue: A1229 - end of helix Processing helix chain 'A' and resid 1230 through 1241 Processing helix chain 'A' and resid 1246 through 1266 removed outlier: 3.580A pdb=" N ARG A1250 " --> pdb=" O VAL A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1289 Processing helix chain 'A' and resid 1291 through 1310 removed outlier: 4.139A pdb=" N PHE A1295 " --> pdb=" O GLU A1291 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP A1308 " --> pdb=" O ALA A1304 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER A1309 " --> pdb=" O ASN A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1328 Processing helix chain 'A' and resid 1346 through 1355 removed outlier: 4.568A pdb=" N PHE A1350 " --> pdb=" O PRO A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1371 removed outlier: 3.904A pdb=" N VAL A1371 " --> pdb=" O ALA A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1374 No H-bonds generated for 'chain 'A' and resid 1372 through 1374' Processing helix chain 'A' and resid 1375 through 1377 No H-bonds generated for 'chain 'A' and resid 1375 through 1377' Processing helix chain 'A' and resid 1378 through 1388 Processing helix chain 'A' and resid 1399 through 1420 removed outlier: 3.606A pdb=" N SER A1420 " --> pdb=" O ALA A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1427 through 1441 removed outlier: 3.785A pdb=" N GLU A1431 " --> pdb=" O ASP A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1447 Processing helix chain 'A' and resid 1452 through 1473 removed outlier: 3.665A pdb=" N ARG A1456 " --> pdb=" O CYS A1452 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A1472 " --> pdb=" O CYS A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1483 through 1496 Processing helix chain 'A' and resid 1497 through 1502 Processing helix chain 'A' and resid 1511 through 1532 Processing helix chain 'A' and resid 1544 through 1549 Processing helix chain 'A' and resid 1553 through 1572 Processing helix chain 'A' and resid 1581 through 1585 removed outlier: 3.859A pdb=" N CYS A1585 " --> pdb=" O PRO A1582 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1598 removed outlier: 3.616A pdb=" N MET A1596 " --> pdb=" O LEU A1592 " (cutoff:3.500A) Processing helix chain 'A' and resid 1600 through 1614 removed outlier: 3.925A pdb=" N LYS A1606 " --> pdb=" O GLU A1602 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1620 removed outlier: 3.753A pdb=" N TRP A1619 " --> pdb=" O ASP A1615 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1627 removed outlier: 3.516A pdb=" N VAL A1627 " --> pdb=" O THR A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1645 Processing helix chain 'A' and resid 1647 through 1668 removed outlier: 3.806A pdb=" N SER A1651 " --> pdb=" O SER A1647 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS A1668 " --> pdb=" O HIS A1664 " (cutoff:3.500A) Processing helix chain 'A' and resid 1670 through 1675 removed outlier: 3.954A pdb=" N LEU A1674 " --> pdb=" O GLU A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1675 through 1690 Processing helix chain 'A' and resid 1695 through 1709 removed outlier: 3.855A pdb=" N ARG A1699 " --> pdb=" O PRO A1695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1709 through 1714 Processing helix chain 'A' and resid 1722 through 1737 Processing helix chain 'A' and resid 1741 through 1757 Processing helix chain 'A' and resid 1773 through 1792 removed outlier: 4.068A pdb=" N ALA A1779 " --> pdb=" O SER A1775 " (cutoff:3.500A) Processing helix chain 'A' and resid 1798 through 1808 Processing helix chain 'A' and resid 1839 through 1859 removed outlier: 3.772A pdb=" N PHE A1843 " --> pdb=" O GLU A1839 " (cutoff:3.500A) Processing helix chain 'A' and resid 1864 through 1888 removed outlier: 4.451A pdb=" N LEU A1868 " --> pdb=" O SER A1864 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS A1870 " --> pdb=" O GLU A1866 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU A1871 " --> pdb=" O MET A1867 " (cutoff:3.500A) Processing helix chain 'A' and resid 1892 through 1897 Processing helix chain 'A' and resid 1897 through 1922 Processing helix chain 'A' and resid 1932 through 1943 Processing helix chain 'B' and resid 11 through 19 removed outlier: 3.747A pdb=" N LYS B 17 " --> pdb=" O TYR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 37 removed outlier: 3.502A pdb=" N LEU B 29 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 63 Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 124 through 147 removed outlier: 3.841A pdb=" N ASP B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 173 removed outlier: 3.565A pdb=" N VAL B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE B 173 " --> pdb=" O GLN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 238 Proline residue: B 234 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 1280 through 1281 removed outlier: 6.493A pdb=" N MET A1280 " --> pdb=" O TYR A1331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.812A pdb=" N ARG B 44 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N VAL B 114 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL B 46 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL B 113 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N LYS B 156 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N CYS B 115 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N PHE B 158 " --> pdb=" O CYS B 115 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TYR B 199 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE B 174 " --> pdb=" O TYR B 199 " (cutoff:3.500A) 1013 hydrogen bonds defined for protein. 3003 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 63 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 3.68 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4273 1.33 - 1.45: 4021 1.45 - 1.58: 9286 1.58 - 1.70: 143 1.70 - 1.82: 163 Bond restraints: 17886 Sorted by residual: bond pdb=" C3' SAH B 401 " pdb=" O3' SAH B 401 " ideal model delta sigma weight residual 1.406 1.362 0.044 2.00e-02 2.50e+03 4.92e+00 bond pdb=" CB THR A 751 " pdb=" CG2 THR A 751 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.61e+00 bond pdb=" CB TRP A1054 " pdb=" CG TRP A1054 " ideal model delta sigma weight residual 1.498 1.450 0.048 3.10e-02 1.04e+03 2.43e+00 bond pdb=" C8 SAH B 401 " pdb=" N7 SAH B 401 " ideal model delta sigma weight residual 1.299 1.330 -0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" CB THR A1120 " pdb=" CG2 THR A1120 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.34e+00 ... (remaining 17881 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 24113 2.04 - 4.08: 419 4.08 - 6.11: 72 6.11 - 8.15: 12 8.15 - 10.19: 2 Bond angle restraints: 24618 Sorted by residual: angle pdb=" N TRP A 400 " pdb=" CA TRP A 400 " pdb=" CB TRP A 400 " ideal model delta sigma weight residual 110.32 117.04 -6.72 1.70e+00 3.46e-01 1.56e+01 angle pdb=" N ASP A 210 " pdb=" CA ASP A 210 " pdb=" C ASP A 210 " ideal model delta sigma weight residual 114.62 110.85 3.77 1.14e+00 7.69e-01 1.09e+01 angle pdb=" C HIS A 399 " pdb=" N TRP A 400 " pdb=" CA TRP A 400 " ideal model delta sigma weight residual 120.60 115.34 5.26 1.60e+00 3.91e-01 1.08e+01 angle pdb=" C ARG A1159 " pdb=" N ARG A1160 " pdb=" CA ARG A1160 " ideal model delta sigma weight residual 121.54 127.75 -6.21 1.91e+00 2.74e-01 1.06e+01 angle pdb=" CG LYS A 56 " pdb=" CD LYS A 56 " pdb=" CE LYS A 56 " ideal model delta sigma weight residual 111.30 103.99 7.31 2.30e+00 1.89e-01 1.01e+01 ... (remaining 24613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 9568 17.66 - 35.33: 944 35.33 - 52.99: 239 52.99 - 70.66: 107 70.66 - 88.32: 36 Dihedral angle restraints: 10894 sinusoidal: 5008 harmonic: 5886 Sorted by residual: dihedral pdb=" CA ASP A 615 " pdb=" C ASP A 615 " pdb=" N THR A 616 " pdb=" CA THR A 616 " ideal model delta harmonic sigma weight residual 180.00 155.79 24.21 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA LEU A1342 " pdb=" C LEU A1342 " pdb=" N SER A1343 " pdb=" CA SER A1343 " ideal model delta harmonic sigma weight residual 180.00 156.02 23.98 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA SER A 612 " pdb=" C SER A 612 " pdb=" N ALA A 613 " pdb=" CA ALA A 613 " ideal model delta harmonic sigma weight residual -180.00 -156.23 -23.77 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 10891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2059 0.045 - 0.089: 701 0.089 - 0.133: 155 0.133 - 0.178: 11 0.178 - 0.222: 4 Chirality restraints: 2930 Sorted by residual: chirality pdb=" CA PHE A 502 " pdb=" N PHE A 502 " pdb=" C PHE A 502 " pdb=" CB PHE A 502 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C2' SAH B 401 " pdb=" C1' SAH B 401 " pdb=" C3' SAH B 401 " pdb=" O2' SAH B 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.74 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA TRP A 400 " pdb=" N TRP A 400 " pdb=" C TRP A 400 " pdb=" CB TRP A 400 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.30e-01 ... (remaining 2927 not shown) Planarity restraints: 2831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 400 " 0.055 2.00e-02 2.50e+03 5.93e-02 8.78e+01 pdb=" CG TRP A 400 " -0.152 2.00e-02 2.50e+03 pdb=" CD1 TRP A 400 " 0.091 2.00e-02 2.50e+03 pdb=" CD2 TRP A 400 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP A 400 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP A 400 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 400 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 400 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 400 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP A 400 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 42 " 0.035 2.00e-02 2.50e+03 1.59e-02 6.94e+00 pdb=" N9 A C 42 " -0.037 2.00e-02 2.50e+03 pdb=" C8 A C 42 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A C 42 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A C 42 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A C 42 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A C 42 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A C 42 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A C 42 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A C 42 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A C 42 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A1345 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A1346 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A1346 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A1346 " -0.035 5.00e-02 4.00e+02 ... (remaining 2828 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 297 2.65 - 3.21: 16954 3.21 - 3.78: 28319 3.78 - 4.34: 38094 4.34 - 4.90: 61609 Nonbonded interactions: 145273 Sorted by model distance: nonbonded pdb=" O TYR B 244 " pdb=" OH TYR B 250 " model vdw 2.091 3.040 nonbonded pdb=" O2' A C 42 " pdb=" O5' A C 43 " model vdw 2.121 3.040 nonbonded pdb=" O ILE A1494 " pdb=" OG SER A1497 " model vdw 2.168 3.040 nonbonded pdb=" ND2 ASN A1124 " pdb=" O SER A1174 " model vdw 2.169 3.120 nonbonded pdb=" O GLN A 76 " pdb=" NH1 ARG A 117 " model vdw 2.189 3.120 ... (remaining 145268 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.420 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.700 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:8.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 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 : 0.008 0.053 17888 Z= 0.346 Angle : 0.696 10.191 24618 Z= 0.366 Chirality : 0.045 0.222 2930 Planarity : 0.005 0.063 2831 Dihedral : 16.551 88.319 7050 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.24 % Favored : 94.71 % Rotamer: Outliers : 0.06 % Allowed : 0.28 % Favored : 99.66 % 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 aren not related in a simple way. whole: 0.96 (0.19), residues: 1985 helix: 1.39 (0.14), residues: 1361 sheet: 0.32 (0.75), residues: 37 loop : -1.09 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 327 TYR 0.013 0.002 TYR A1167 PHE 0.019 0.002 PHE A1428 TRP 0.152 0.003 TRP A 400 HIS 0.011 0.001 HIS A1209 Details of bonding type rmsd covalent geometry : bond 0.00805 (17886) covalent geometry : angle 0.69595 (24618) hydrogen bonds : bond 0.15078 ( 1076) hydrogen bonds : angle 5.62597 ( 3105) metal coordination : bond 0.00119 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.574 Fit side-chains REVERT: A 70 MET cc_start: 0.5905 (tmm) cc_final: 0.5612 (tmm) REVERT: A 112 PRO cc_start: 0.7688 (Cg_exo) cc_final: 0.7316 (Cg_endo) REVERT: A 115 MET cc_start: 0.7273 (mmp) cc_final: 0.6847 (tmm) REVERT: A 149 ASN cc_start: 0.7921 (m-40) cc_final: 0.7636 (m110) REVERT: A 152 ARG cc_start: 0.6310 (mtp-110) cc_final: 0.6061 (mtp85) REVERT: A 189 GLN cc_start: 0.7817 (mt0) cc_final: 0.7490 (tp-100) REVERT: A 354 MET cc_start: 0.7280 (ttp) cc_final: 0.7057 (tpt) REVERT: A 421 MET cc_start: 0.9031 (mtp) cc_final: 0.8796 (mtp) REVERT: A 1803 LEU cc_start: 0.8567 (mp) cc_final: 0.8333 (mm) REVERT: B 44 ARG cc_start: 0.8174 (mtp85) cc_final: 0.7944 (mtp85) REVERT: B 104 HIS cc_start: 0.8077 (m-70) cc_final: 0.7640 (m-70) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.7248 time to fit residues: 136.4863 Evaluate side-chains 118 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 10.0000 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 104 ASN ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN A 541 GLN A1132 GLN A1409 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.138208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.096262 restraints weight = 31791.256| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.79 r_work: 0.3004 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17888 Z= 0.149 Angle : 0.611 9.759 24618 Z= 0.313 Chirality : 0.039 0.220 2930 Planarity : 0.004 0.066 2831 Dihedral : 14.666 81.290 3258 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.73 % Allowed : 5.82 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.19), residues: 1985 helix: 1.89 (0.14), residues: 1375 sheet: 0.46 (0.81), residues: 37 loop : -1.01 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 117 TYR 0.014 0.001 TYR A 86 PHE 0.047 0.001 PHE A 502 TRP 0.066 0.002 TRP A 400 HIS 0.006 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00326 (17886) covalent geometry : angle 0.61143 (24618) hydrogen bonds : bond 0.05668 ( 1076) hydrogen bonds : angle 4.10316 ( 3105) metal coordination : bond 0.00098 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.555 Fit side-chains REVERT: A 115 MET cc_start: 0.7211 (mmp) cc_final: 0.6835 (tmm) REVERT: A 116 HIS cc_start: 0.7209 (OUTLIER) cc_final: 0.6702 (p90) REVERT: A 152 ARG cc_start: 0.6170 (mtp-110) cc_final: 0.5826 (mtp85) REVERT: A 189 GLN cc_start: 0.7906 (mt0) cc_final: 0.7554 (mp10) REVERT: A 354 MET cc_start: 0.8208 (ttp) cc_final: 0.7365 (tpt) REVERT: A 421 MET cc_start: 0.8876 (mtp) cc_final: 0.8517 (mtp) REVERT: A 439 GLU cc_start: 0.7915 (tp30) cc_final: 0.7660 (tm-30) REVERT: B 35 GLU cc_start: 0.8225 (tt0) cc_final: 0.8000 (tt0) REVERT: B 62 LYS cc_start: 0.8342 (ttmm) cc_final: 0.7963 (ttmm) REVERT: B 104 HIS cc_start: 0.7873 (m-70) cc_final: 0.7439 (m-70) REVERT: B 145 HIS cc_start: 0.8180 (OUTLIER) cc_final: 0.7732 (m-70) outliers start: 12 outliers final: 4 residues processed: 140 average time/residue: 0.7596 time to fit residues: 117.2383 Evaluate side-chains 123 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 1428 PHE Chi-restraints excluded: chain A residue 1664 HIS Chi-restraints excluded: chain A residue 1903 ARG Chi-restraints excluded: chain B residue 145 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 6 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 0.0970 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 GLN ** A1278 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 = 0.3800 r_free = 0.3800 target = 0.138122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.095881 restraints weight = 33660.369| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.60 r_work: 0.3004 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17888 Z= 0.163 Angle : 0.589 9.406 24618 Z= 0.300 Chirality : 0.039 0.194 2930 Planarity : 0.004 0.066 2831 Dihedral : 14.566 81.293 3258 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.90 % Allowed : 8.01 % Favored : 91.10 % 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 aren not related in a simple way. whole: 1.70 (0.19), residues: 1985 helix: 2.02 (0.14), residues: 1376 sheet: 0.31 (0.70), residues: 45 loop : -1.08 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 117 TYR 0.013 0.001 TYR A 134 PHE 0.043 0.001 PHE A 502 TRP 0.058 0.002 TRP A 400 HIS 0.006 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00373 (17886) covalent geometry : angle 0.58888 (24618) hydrogen bonds : bond 0.05438 ( 1076) hydrogen bonds : angle 3.93212 ( 3105) metal coordination : bond 0.00004 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.683 Fit side-chains REVERT: A 115 MET cc_start: 0.7246 (mmp) cc_final: 0.6835 (tmm) REVERT: A 116 HIS cc_start: 0.7193 (OUTLIER) cc_final: 0.6640 (p90) REVERT: A 152 ARG cc_start: 0.6246 (mtp-110) cc_final: 0.5941 (mtp85) REVERT: A 189 GLN cc_start: 0.7962 (mt0) cc_final: 0.7606 (mp10) REVERT: A 354 MET cc_start: 0.8441 (ttp) cc_final: 0.7570 (tpt) REVERT: A 421 MET cc_start: 0.8909 (mtp) cc_final: 0.8615 (mtp) REVERT: A 439 GLU cc_start: 0.8195 (tp30) cc_final: 0.7808 (tm-30) REVERT: B 35 GLU cc_start: 0.8248 (tt0) cc_final: 0.7955 (tt0) REVERT: B 100 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7666 (tp30) REVERT: B 104 HIS cc_start: 0.7952 (m-70) cc_final: 0.7374 (m-70) REVERT: B 145 HIS cc_start: 0.8282 (OUTLIER) cc_final: 0.7873 (m-70) REVERT: B 147 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7395 (pt) REVERT: B 200 ASP cc_start: 0.7845 (t70) cc_final: 0.7353 (t0) outliers start: 15 outliers final: 4 residues processed: 138 average time/residue: 0.7825 time to fit residues: 119.0411 Evaluate side-chains 124 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 1054 TRP Chi-restraints excluded: chain A residue 1903 ARG Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 147 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 77 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 175 optimal weight: 8.9990 chunk 193 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 145 optimal weight: 0.0000 chunk 72 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 GLN ** A1278 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 = 0.3821 r_free = 0.3821 target = 0.139774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.098363 restraints weight = 25524.349| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.16 r_work: 0.3070 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17888 Z= 0.133 Angle : 0.557 9.448 24618 Z= 0.284 Chirality : 0.038 0.194 2930 Planarity : 0.004 0.066 2831 Dihedral : 14.542 80.864 3258 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.01 % Allowed : 9.46 % Favored : 89.53 % 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 aren not related in a simple way. whole: 1.84 (0.19), residues: 1985 helix: 2.12 (0.14), residues: 1379 sheet: 0.37 (0.72), residues: 45 loop : -1.04 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 44 TYR 0.010 0.001 TYR A 563 PHE 0.043 0.001 PHE A1428 TRP 0.042 0.001 TRP A 400 HIS 0.007 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00295 (17886) covalent geometry : angle 0.55650 (24618) hydrogen bonds : bond 0.04831 ( 1076) hydrogen bonds : angle 3.79122 ( 3105) metal coordination : bond 0.00007 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.598 Fit side-chains REVERT: A 116 HIS cc_start: 0.7191 (OUTLIER) cc_final: 0.6742 (p90) REVERT: A 152 ARG cc_start: 0.6139 (mtp-110) cc_final: 0.5880 (mtp85) REVERT: A 354 MET cc_start: 0.8406 (ttp) cc_final: 0.7543 (tpt) REVERT: A 439 GLU cc_start: 0.8159 (tp30) cc_final: 0.7799 (tm-30) REVERT: A 1597 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8183 (tttp) REVERT: B 35 GLU cc_start: 0.8247 (tt0) cc_final: 0.7985 (tt0) REVERT: B 104 HIS cc_start: 0.7994 (m-70) cc_final: 0.7373 (m-70) REVERT: B 145 HIS cc_start: 0.8256 (OUTLIER) cc_final: 0.7845 (m-70) REVERT: B 147 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7448 (pt) REVERT: B 200 ASP cc_start: 0.7799 (t70) cc_final: 0.7410 (t0) outliers start: 17 outliers final: 6 residues processed: 134 average time/residue: 0.6901 time to fit residues: 102.5019 Evaluate side-chains 128 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 1054 TRP Chi-restraints excluded: chain A residue 1375 MET Chi-restraints excluded: chain A residue 1664 HIS Chi-restraints excluded: chain A residue 1853 CYS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 147 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 116 optimal weight: 0.0270 chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 0.0270 chunk 51 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 overall best weight: 0.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 184 HIS ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1791 GLN B 169 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.141734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.099207 restraints weight = 38249.540| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.98 r_work: 0.3044 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17888 Z= 0.113 Angle : 0.531 9.267 24618 Z= 0.269 Chirality : 0.037 0.243 2930 Planarity : 0.004 0.065 2831 Dihedral : 14.499 80.158 3258 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.95 % Allowed : 9.85 % Favored : 89.19 % 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 aren not related in a simple way. whole: 2.01 (0.19), residues: 1985 helix: 2.24 (0.14), residues: 1380 sheet: 0.46 (0.73), residues: 45 loop : -0.98 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 44 TYR 0.016 0.001 TYR A 134 PHE 0.037 0.001 PHE A 502 TRP 0.031 0.001 TRP A 400 HIS 0.012 0.001 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00242 (17886) covalent geometry : angle 0.53079 (24618) hydrogen bonds : bond 0.04315 ( 1076) hydrogen bonds : angle 3.67139 ( 3105) metal coordination : bond 0.00002 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.585 Fit side-chains REVERT: A 99 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7225 (pp) REVERT: A 115 MET cc_start: 0.7197 (mmp) cc_final: 0.6758 (tmm) REVERT: A 116 HIS cc_start: 0.7180 (OUTLIER) cc_final: 0.6530 (p90) REVERT: A 152 ARG cc_start: 0.6017 (mtp-110) cc_final: 0.5787 (mtp85) REVERT: A 178 ARG cc_start: 0.8317 (ttp-110) cc_final: 0.7915 (ttm110) REVERT: A 439 GLU cc_start: 0.7981 (tp30) cc_final: 0.7651 (tm-30) REVERT: A 913 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8122 (pt0) REVERT: A 1597 LYS cc_start: 0.8588 (ttmt) cc_final: 0.8162 (tttp) REVERT: A 1602 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7897 (tm-30) REVERT: B 35 GLU cc_start: 0.8175 (tt0) cc_final: 0.7910 (tt0) REVERT: B 100 GLU cc_start: 0.7998 (tp30) cc_final: 0.7656 (tt0) REVERT: B 104 HIS cc_start: 0.8042 (m-70) cc_final: 0.7564 (m-70) REVERT: B 145 HIS cc_start: 0.8154 (OUTLIER) cc_final: 0.7864 (m-70) REVERT: B 147 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7309 (pt) REVERT: B 200 ASP cc_start: 0.7768 (t70) cc_final: 0.7358 (m-30) outliers start: 16 outliers final: 4 residues processed: 132 average time/residue: 0.7055 time to fit residues: 102.8247 Evaluate side-chains 123 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 1054 TRP Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 147 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 183 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 147 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 84 optimal weight: 0.1980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 541 GLN B 145 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.140639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.099199 restraints weight = 25891.529| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.17 r_work: 0.3090 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17888 Z= 0.130 Angle : 0.553 10.446 24618 Z= 0.278 Chirality : 0.038 0.345 2930 Planarity : 0.004 0.076 2831 Dihedral : 14.473 80.912 3258 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.01 % Allowed : 10.25 % Favored : 88.75 % 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 aren not related in a simple way. whole: 2.01 (0.19), residues: 1985 helix: 2.25 (0.14), residues: 1379 sheet: 0.46 (0.73), residues: 45 loop : -0.99 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 117 TYR 0.010 0.001 TYR B 199 PHE 0.037 0.001 PHE A 502 TRP 0.030 0.001 TRP A 400 HIS 0.011 0.001 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00292 (17886) covalent geometry : angle 0.55334 (24618) hydrogen bonds : bond 0.04560 ( 1076) hydrogen bonds : angle 3.68290 ( 3105) metal coordination : bond 0.00018 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.678 Fit side-chains REVERT: A 115 MET cc_start: 0.7221 (mmp) cc_final: 0.6769 (ppp) REVERT: A 116 HIS cc_start: 0.7199 (OUTLIER) cc_final: 0.6604 (p90) REVERT: A 152 ARG cc_start: 0.6086 (mtp-110) cc_final: 0.5878 (mtp85) REVERT: A 354 MET cc_start: 0.8396 (ttp) cc_final: 0.7511 (tpt) REVERT: A 485 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8816 (mmm) REVERT: A 598 MET cc_start: 0.8899 (mmt) cc_final: 0.8664 (mmt) REVERT: A 913 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8210 (pt0) REVERT: A 1597 LYS cc_start: 0.8616 (ttmt) cc_final: 0.8201 (tttp) REVERT: B 35 GLU cc_start: 0.8277 (tt0) cc_final: 0.8019 (tt0) REVERT: B 100 GLU cc_start: 0.8120 (tp30) cc_final: 0.7706 (tt0) REVERT: B 104 HIS cc_start: 0.8081 (m-70) cc_final: 0.7612 (m-70) REVERT: B 147 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7437 (pt) REVERT: B 200 ASP cc_start: 0.7821 (t70) cc_final: 0.7432 (m-30) outliers start: 17 outliers final: 6 residues processed: 124 average time/residue: 0.7385 time to fit residues: 101.1086 Evaluate side-chains 122 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 1054 TRP Chi-restraints excluded: chain A residue 1344 MET Chi-restraints excluded: chain A residue 1375 MET Chi-restraints excluded: chain B residue 147 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 23 optimal weight: 2.9990 chunk 116 optimal weight: 0.0870 chunk 147 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 189 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 43 optimal weight: 0.0970 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 789 GLN ** A 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 145 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.141071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.099568 restraints weight = 25813.301| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.18 r_work: 0.3090 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17888 Z= 0.123 Angle : 0.542 10.561 24618 Z= 0.273 Chirality : 0.038 0.343 2930 Planarity : 0.004 0.071 2831 Dihedral : 14.467 80.533 3258 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.78 % Allowed : 10.53 % Favored : 88.69 % 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 aren not related in a simple way. whole: 2.09 (0.19), residues: 1985 helix: 2.30 (0.14), residues: 1379 sheet: 0.50 (0.73), residues: 45 loop : -0.95 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 117 TYR 0.016 0.001 TYR B 167 PHE 0.036 0.001 PHE A 502 TRP 0.028 0.001 TRP A 400 HIS 0.010 0.001 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00273 (17886) covalent geometry : angle 0.54247 (24618) hydrogen bonds : bond 0.04421 ( 1076) hydrogen bonds : angle 3.65137 ( 3105) metal coordination : bond 0.00008 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.551 Fit side-chains REVERT: A 115 MET cc_start: 0.7219 (mmp) cc_final: 0.6760 (ppp) REVERT: A 116 HIS cc_start: 0.7209 (OUTLIER) cc_final: 0.6630 (p90) REVERT: A 152 ARG cc_start: 0.6035 (mtp-110) cc_final: 0.5825 (mtp85) REVERT: A 354 MET cc_start: 0.8394 (ttp) cc_final: 0.7525 (tpt) REVERT: A 485 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8845 (mmm) REVERT: A 1597 LYS cc_start: 0.8588 (ttmt) cc_final: 0.8193 (tttp) REVERT: A 1602 GLU cc_start: 0.8296 (tm-30) cc_final: 0.8060 (tm-30) REVERT: B 35 GLU cc_start: 0.8269 (tt0) cc_final: 0.8020 (tt0) REVERT: B 100 GLU cc_start: 0.8226 (tp30) cc_final: 0.7652 (tt0) REVERT: B 104 HIS cc_start: 0.8067 (m-70) cc_final: 0.7601 (m-70) REVERT: B 147 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7299 (pt) REVERT: B 200 ASP cc_start: 0.7801 (t70) cc_final: 0.7441 (m-30) outliers start: 13 outliers final: 5 residues processed: 129 average time/residue: 0.6931 time to fit residues: 99.1164 Evaluate side-chains 122 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 1054 TRP Chi-restraints excluded: chain A residue 1639 MET Chi-restraints excluded: chain B residue 147 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 156 optimal weight: 0.0570 chunk 141 optimal weight: 0.1980 chunk 113 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 195 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 184 HIS ** A 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.143415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.102401 restraints weight = 28260.170| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.63 r_work: 0.3115 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17888 Z= 0.107 Angle : 0.526 10.960 24618 Z= 0.263 Chirality : 0.037 0.350 2930 Planarity : 0.004 0.065 2831 Dihedral : 14.462 79.788 3258 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.62 % Allowed : 11.03 % Favored : 88.35 % 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 aren not related in a simple way. whole: 2.20 (0.20), residues: 1985 helix: 2.40 (0.14), residues: 1379 sheet: 0.59 (0.74), residues: 45 loop : -0.94 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 117 TYR 0.009 0.001 TYR A 563 PHE 0.035 0.001 PHE A 502 TRP 0.023 0.001 TRP A 400 HIS 0.011 0.001 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00223 (17886) covalent geometry : angle 0.52551 (24618) hydrogen bonds : bond 0.03978 ( 1076) hydrogen bonds : angle 3.58189 ( 3105) metal coordination : bond 0.00005 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.495 Fit side-chains REVERT: A 115 MET cc_start: 0.7198 (mmp) cc_final: 0.6705 (pp-130) REVERT: A 116 HIS cc_start: 0.7214 (OUTLIER) cc_final: 0.6604 (p90) REVERT: A 152 ARG cc_start: 0.5957 (mtp-110) cc_final: 0.5754 (mtp85) REVERT: A 354 MET cc_start: 0.8370 (ttp) cc_final: 0.7462 (tpt) REVERT: A 598 MET cc_start: 0.8868 (mmt) cc_final: 0.8584 (mmt) REVERT: A 913 GLN cc_start: 0.8542 (pt0) cc_final: 0.8187 (tt0) REVERT: A 1597 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8167 (tttp) REVERT: B 35 GLU cc_start: 0.8214 (tt0) cc_final: 0.7985 (tt0) REVERT: B 100 GLU cc_start: 0.8245 (tp30) cc_final: 0.7607 (tt0) REVERT: B 104 HIS cc_start: 0.7952 (m-70) cc_final: 0.7410 (m-70) REVERT: B 147 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7302 (pt) REVERT: B 200 ASP cc_start: 0.7778 (t70) cc_final: 0.7433 (m-30) outliers start: 10 outliers final: 8 residues processed: 128 average time/residue: 0.6731 time to fit residues: 95.5478 Evaluate side-chains 123 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 1054 TRP Chi-restraints excluded: chain A residue 1375 MET Chi-restraints excluded: chain A residue 1639 MET Chi-restraints excluded: chain A residue 1853 CYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 147 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 84 optimal weight: 0.0020 chunk 63 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 130 optimal weight: 0.0970 chunk 115 optimal weight: 2.9990 chunk 151 optimal weight: 0.0170 chunk 179 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.2228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 720 HIS ** A 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.141560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.099508 restraints weight = 33298.902| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.72 r_work: 0.3065 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17888 Z= 0.123 Angle : 0.544 11.980 24618 Z= 0.272 Chirality : 0.038 0.357 2930 Planarity : 0.004 0.065 2831 Dihedral : 14.435 81.041 3258 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.78 % Allowed : 10.92 % Favored : 88.30 % 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 aren not related in a simple way. whole: 2.20 (0.19), residues: 1985 helix: 2.39 (0.14), residues: 1378 sheet: 0.61 (0.73), residues: 45 loop : -0.92 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 178 TYR 0.014 0.001 TYR B 167 PHE 0.035 0.001 PHE A 502 TRP 0.026 0.001 TRP A 400 HIS 0.012 0.001 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00275 (17886) covalent geometry : angle 0.54430 (24618) hydrogen bonds : bond 0.04354 ( 1076) hydrogen bonds : angle 3.59965 ( 3105) metal coordination : bond 0.00013 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.608 Fit side-chains REVERT: A 70 MET cc_start: 0.6033 (OUTLIER) cc_final: 0.5797 (tmm) REVERT: A 115 MET cc_start: 0.7186 (mmp) cc_final: 0.6681 (pp-130) REVERT: A 116 HIS cc_start: 0.7211 (OUTLIER) cc_final: 0.6595 (p90) REVERT: A 152 ARG cc_start: 0.5957 (mtp-110) cc_final: 0.5505 (mmt180) REVERT: A 354 MET cc_start: 0.8148 (ttp) cc_final: 0.7295 (tpt) REVERT: A 421 MET cc_start: 0.8812 (mtp) cc_final: 0.8547 (mtp) REVERT: A 598 MET cc_start: 0.8752 (mmt) cc_final: 0.8497 (mmt) REVERT: A 913 GLN cc_start: 0.8474 (pt0) cc_final: 0.8146 (tt0) REVERT: A 1430 HIS cc_start: 0.7516 (m90) cc_final: 0.7314 (m90) REVERT: A 1597 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8162 (tttp) REVERT: A 1666 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6498 (mt0) REVERT: B 35 GLU cc_start: 0.8142 (tt0) cc_final: 0.7906 (tt0) REVERT: B 100 GLU cc_start: 0.8293 (tp30) cc_final: 0.7669 (tt0) REVERT: B 104 HIS cc_start: 0.7946 (m-70) cc_final: 0.7439 (m-70) REVERT: B 147 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7291 (pt) REVERT: B 200 ASP cc_start: 0.7726 (t70) cc_final: 0.7401 (m-30) outliers start: 13 outliers final: 6 residues processed: 121 average time/residue: 0.7293 time to fit residues: 97.3892 Evaluate side-chains 124 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 1054 TRP Chi-restraints excluded: chain A residue 1375 MET Chi-restraints excluded: chain A residue 1639 MET Chi-restraints excluded: chain A residue 1666 GLN Chi-restraints excluded: chain B residue 147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 88 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 202 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 201 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 720 HIS ** A 819 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 = 0.3825 r_free = 0.3825 target = 0.140178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.098840 restraints weight = 25750.630| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.40 r_work: 0.3064 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17888 Z= 0.141 Angle : 0.562 12.447 24618 Z= 0.281 Chirality : 0.039 0.364 2930 Planarity : 0.004 0.064 2831 Dihedral : 14.450 81.090 3258 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.67 % Allowed : 11.37 % Favored : 87.96 % 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 aren not related in a simple way. whole: 2.12 (0.19), residues: 1985 helix: 2.31 (0.14), residues: 1381 sheet: 0.52 (0.73), residues: 45 loop : -0.90 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 178 TYR 0.010 0.001 TYR A1459 PHE 0.036 0.001 PHE A 502 TRP 0.028 0.001 TRP A 400 HIS 0.012 0.001 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00322 (17886) covalent geometry : angle 0.56210 (24618) hydrogen bonds : bond 0.04731 ( 1076) hydrogen bonds : angle 3.66247 ( 3105) metal coordination : bond 0.00018 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.657 Fit side-chains REVERT: A 70 MET cc_start: 0.6051 (OUTLIER) cc_final: 0.5816 (tmm) REVERT: A 115 MET cc_start: 0.7193 (mmp) cc_final: 0.6723 (ppp) REVERT: A 116 HIS cc_start: 0.7247 (OUTLIER) cc_final: 0.6672 (p90) REVERT: A 152 ARG cc_start: 0.6059 (mtp-110) cc_final: 0.5586 (mmt180) REVERT: A 354 MET cc_start: 0.8409 (ttp) cc_final: 0.7554 (tpt) REVERT: A 421 MET cc_start: 0.8903 (mtp) cc_final: 0.8602 (mtp) REVERT: A 913 GLN cc_start: 0.8574 (pt0) cc_final: 0.8229 (tt0) REVERT: A 1430 HIS cc_start: 0.7678 (m90) cc_final: 0.7450 (m90) REVERT: A 1597 LYS cc_start: 0.8593 (ttmt) cc_final: 0.8212 (tttp) REVERT: A 1666 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6709 (mt0) REVERT: B 35 GLU cc_start: 0.8238 (tt0) cc_final: 0.7974 (tt0) REVERT: B 100 GLU cc_start: 0.8357 (tp30) cc_final: 0.7725 (tt0) REVERT: B 104 HIS cc_start: 0.7939 (m-70) cc_final: 0.7381 (m-70) REVERT: B 147 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7327 (pt) REVERT: B 200 ASP cc_start: 0.7821 (t70) cc_final: 0.7503 (m-30) outliers start: 11 outliers final: 6 residues processed: 122 average time/residue: 0.7735 time to fit residues: 104.1854 Evaluate side-chains 126 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 1054 TRP Chi-restraints excluded: chain A residue 1639 MET Chi-restraints excluded: chain A residue 1666 GLN Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 36 optimal weight: 0.0070 chunk 111 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 47 optimal weight: 0.0070 chunk 1 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 chunk 206 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 720 HIS A 819 HIS A 913 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.142274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.099508 restraints weight = 33263.291| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.94 r_work: 0.3064 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17888 Z= 0.110 Angle : 0.534 11.594 24618 Z= 0.267 Chirality : 0.037 0.363 2930 Planarity : 0.004 0.065 2831 Dihedral : 14.446 79.550 3258 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.73 % Allowed : 11.53 % Favored : 87.74 % 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 aren not related in a simple way. whole: 2.22 (0.20), residues: 1985 helix: 2.40 (0.14), residues: 1379 sheet: 0.60 (0.72), residues: 45 loop : -0.90 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 44 TYR 0.010 0.001 TYR A 563 PHE 0.035 0.001 PHE A 502 TRP 0.023 0.001 TRP A 400 HIS 0.012 0.001 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00235 (17886) covalent geometry : angle 0.53427 (24618) hydrogen bonds : bond 0.04106 ( 1076) hydrogen bonds : angle 3.56891 ( 3105) metal coordination : bond 0.00013 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7232.50 seconds wall clock time: 123 minutes 38.74 seconds (7418.74 seconds total)