Starting phenix.real_space_refine on Mon Jun 16 23:10:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qen_18373/06_2025/8qen_18373.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qen_18373/06_2025/8qen_18373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qen_18373/06_2025/8qen_18373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qen_18373/06_2025/8qen_18373.map" model { file = "/net/cci-nas-00/data/ceres_data/8qen_18373/06_2025/8qen_18373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qen_18373/06_2025/8qen_18373.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.015 sd= 0.042 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 53 5.16 5 C 12122 2.51 5 N 2981 2.21 5 O 3850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19007 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 19006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2363, 19006 Classifications: {'peptide': 2363} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 2310} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5669 SG CYS A 698 35.399 91.469 183.956 1.00 14.16 S Time building chain proxies: 13.03, per 1000 atoms: 0.69 Number of scatterers: 19007 At special positions: 0 Unit cell: (86.94, 142.582, 224.885, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 53 16.00 O 3850 8.00 N 2981 7.00 C 12122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.63 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2801 " pdb="ZN ZN A2801 " - pdb=" NE2 HIS A 757 " pdb="ZN ZN A2801 " - pdb=" ND1 HIS A 653 " pdb="ZN ZN A2801 " - pdb=" SG CYS A 698 " 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4452 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 40 sheets defined 32.6% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 41 through 63 Processing helix chain 'A' and resid 68 through 90 removed outlier: 3.620A pdb=" N ASN A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 122 Processing helix chain 'A' and resid 137 through 157 Processing helix chain 'A' and resid 158 through 161 removed outlier: 3.968A pdb=" N LEU A 161 " --> pdb=" O ARG A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 158 through 161' Processing helix chain 'A' and resid 167 through 197 Processing helix chain 'A' and resid 201 through 214 Processing helix chain 'A' and resid 217 through 235 removed outlier: 3.802A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 264 through 280 Processing helix chain 'A' and resid 308 through 325 Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 339 through 352 Processing helix chain 'A' and resid 355 through 359 Processing helix chain 'A' and resid 393 through 420 Proline residue: A 416 - end of helix removed outlier: 3.569A pdb=" N GLU A 420 " --> pdb=" O PRO A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 438 Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 451 through 456 removed outlier: 4.995A pdb=" N LEU A 454 " --> pdb=" O GLY A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 470 through 483 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 512 through 519 Processing helix chain 'A' and resid 523 through 537 Processing helix chain 'A' and resid 545 through 549 removed outlier: 3.780A pdb=" N ASN A 548 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 564 Processing helix chain 'A' and resid 587 through 601 removed outlier: 3.983A pdb=" N THR A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 683 Processing helix chain 'A' and resid 706 through 709 Processing helix chain 'A' and resid 710 through 727 removed outlier: 3.506A pdb=" N LYS A 718 " --> pdb=" O LYS A 714 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASP A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 733 No H-bonds generated for 'chain 'A' and resid 731 through 733' Processing helix chain 'A' and resid 764 through 774 Processing helix chain 'A' and resid 793 through 809 Processing helix chain 'A' and resid 814 through 838 Processing helix chain 'A' and resid 846 through 876 Processing helix chain 'A' and resid 886 through 889 removed outlier: 3.911A pdb=" N ILE A 889 " --> pdb=" O PHE A 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 889' Processing helix chain 'A' and resid 916 through 934 Processing helix chain 'A' and resid 951 through 971 Processing helix chain 'A' and resid 975 through 980 Processing helix chain 'A' and resid 980 through 995 Processing helix chain 'A' and resid 997 through 1001 Processing helix chain 'A' and resid 1003 through 1017 Processing helix chain 'A' and resid 1025 through 1029 removed outlier: 4.263A pdb=" N GLY A1028 " --> pdb=" O LEU A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1045 Processing helix chain 'A' and resid 1045 through 1050 removed outlier: 3.697A pdb=" N GLU A1050 " --> pdb=" O LYS A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1064 Processing helix chain 'A' and resid 1072 through 1082 Processing helix chain 'A' and resid 1119 through 1129 Processing helix chain 'A' and resid 1129 through 1134 Processing helix chain 'A' and resid 1180 through 1184 removed outlier: 3.727A pdb=" N ILE A1184 " --> pdb=" O THR A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1206 Processing helix chain 'A' and resid 1245 through 1258 Processing helix chain 'A' and resid 1305 through 1310 Processing helix chain 'A' and resid 1371 through 1375 removed outlier: 3.594A pdb=" N LEU A1375 " --> pdb=" O LEU A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1439 Processing helix chain 'A' and resid 1439 through 1450 Processing helix chain 'A' and resid 1558 through 1572 Processing helix chain 'A' and resid 1579 through 1588 removed outlier: 3.729A pdb=" N SER A1583 " --> pdb=" O ASP A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1679 through 1682 Processing helix chain 'A' and resid 1684 through 1688 Processing helix chain 'A' and resid 1736 through 1738 No H-bonds generated for 'chain 'A' and resid 1736 through 1738' Processing helix chain 'A' and resid 1773 through 1779 Processing helix chain 'A' and resid 1792 through 1799 removed outlier: 3.863A pdb=" N LEU A1797 " --> pdb=" O SER A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 2061 through 2065 Processing helix chain 'A' and resid 2336 through 2340 removed outlier: 3.587A pdb=" N TYR A2339 " --> pdb=" O THR A2336 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 239 removed outlier: 5.931A pdb=" N LEU A 98 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE A 130 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N PHE A 100 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL A 101 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 376 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLN A 385 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N LYS A 374 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 291 removed outlier: 3.507A pdb=" N LEU A 290 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 581 through 583 removed outlier: 7.116A pdb=" N VAL A 582 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N HIS A 653 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N CYS A 698 " --> pdb=" O GLY A 652 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 606 through 608 Processing sheet with id=AA6, first strand: chain 'A' and resid 744 through 746 Processing sheet with id=AA7, first strand: chain 'A' and resid 777 through 781 removed outlier: 4.172A pdb=" N TYR A 777 " --> pdb=" O LYS A 790 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 882 through 884 Processing sheet with id=AA9, first strand: chain 'A' and resid 882 through 884 Processing sheet with id=AB1, first strand: chain 'A' and resid 937 through 938 Processing sheet with id=AB2, first strand: chain 'A' and resid 1066 through 1067 removed outlier: 4.283A pdb=" N VAL A1516 " --> pdb=" O THR A1528 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR A1528 " --> pdb=" O VAL A1516 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL A1518 " --> pdb=" O ILE A1526 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE A1526 " --> pdb=" O VAL A1518 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR A1520 " --> pdb=" O VAL A1524 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL A1524 " --> pdb=" O THR A1520 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ASN A1525 " --> pdb=" O LEU A1544 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU A1544 " --> pdb=" O ASN A1525 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LYS A1537 " --> pdb=" O LEU A1557 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU A1557 " --> pdb=" O LYS A1537 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER A1539 " --> pdb=" O VAL A1555 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL A1555 " --> pdb=" O SER A1539 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER A1541 " --> pdb=" O ASN A1553 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N SER A1554 " --> pdb=" O ASP A1607 " (cutoff:3.500A) removed outlier: 11.122A pdb=" N ASN A1609 " --> pdb=" O SER A1554 " (cutoff:3.500A) removed outlier: 11.160A pdb=" N HIS A1556 " --> pdb=" O ASN A1609 " (cutoff:3.500A) removed outlier: 10.783A pdb=" N ILE A1611 " --> pdb=" O HIS A1556 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N PHE A1610 " --> pdb=" O CYS A1625 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN A1620 " --> pdb=" O ILE A1636 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE A1636 " --> pdb=" O GLN A1620 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU A1622 " --> pdb=" O TYR A1634 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR A1648 " --> pdb=" O ASN A1654 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ASN A1654 " --> pdb=" O TYR A1648 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL A1717 " --> pdb=" O ARG A1766 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR A1800 " --> pdb=" O TYR A1740 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1105 through 1106 Processing sheet with id=AB4, first strand: chain 'A' and resid 1136 through 1140 removed outlier: 6.869A pdb=" N ILE A1143 " --> pdb=" O LEU A1139 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG A1296 " --> pdb=" O ALA A1324 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N SER A1326 " --> pdb=" O ARG A1296 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE A1298 " --> pdb=" O SER A1326 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE A1401 " --> pdb=" O ASP A1342 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N TRP A1344 " --> pdb=" O PHE A1401 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE A1412 " --> pdb=" O ILE A1408 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1161 through 1164 removed outlier: 6.490A pdb=" N SER A1153 " --> pdb=" O ARG A1288 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASN A1290 " --> pdb=" O SER A1153 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A1155 " --> pdb=" O ASN A1290 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR A1285 " --> pdb=" O SER A1313 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N SER A1315 " --> pdb=" O THR A1285 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A1287 " --> pdb=" O SER A1315 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N TYR A1317 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE A1289 " --> pdb=" O TYR A1317 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N ASN A1335 " --> pdb=" O LEU A1312 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR A1314 " --> pdb=" O ASN A1335 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLU A1337 " --> pdb=" O TYR A1314 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE A1316 " --> pdb=" O GLU A1337 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A1334 " --> pdb=" O GLU A1388 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1200 through 1201 removed outlier: 6.914A pdb=" N GLU A1168 " --> pdb=" O PHE A1230 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N TRP A1232 " --> pdb=" O GLU A1168 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN A1227 " --> pdb=" O TYR A1282 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR A1282 " --> pdb=" O ASN A1227 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A1229 " --> pdb=" O PRO A1280 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA A1231 " --> pdb=" O LEU A1278 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU A1278 " --> pdb=" O ALA A1231 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU A1233 " --> pdb=" O THR A1276 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1172 through 1173 Processing sheet with id=AB8, first strand: chain 'A' and resid 1353 through 1358 removed outlier: 4.611A pdb=" N ASP A1354 " --> pdb=" O GLY A1365 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1459 through 1466 removed outlier: 4.177A pdb=" N GLU A1481 " --> pdb=" O ASN A1476 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1673 through 1677 removed outlier: 6.416A pdb=" N ILE A1674 " --> pdb=" O ASN A1703 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N THR A1705 " --> pdb=" O ILE A1674 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N PHE A1676 " --> pdb=" O THR A1705 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1834 through 1838 Processing sheet with id=AC3, first strand: chain 'A' and resid 1855 through 1857 removed outlier: 3.554A pdb=" N ALA A1873 " --> pdb=" O ASN A1867 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1877 through 1881 Processing sheet with id=AC5, first strand: chain 'A' and resid 1898 through 1901 Processing sheet with id=AC6, first strand: chain 'A' and resid 1927 through 1931 Processing sheet with id=AC7, first strand: chain 'A' and resid 1968 through 1972 Processing sheet with id=AC8, first strand: chain 'A' and resid 1988 through 1992 Processing sheet with id=AC9, first strand: chain 'A' and resid 2008 through 2012 Processing sheet with id=AD1, first strand: chain 'A' and resid 2028 through 2031 Processing sheet with id=AD2, first strand: chain 'A' and resid 2058 through 2060 Processing sheet with id=AD3, first strand: chain 'A' and resid 2078 through 2081 Processing sheet with id=AD4, first strand: chain 'A' and resid 2100 through 2102 Processing sheet with id=AD5, first strand: chain 'A' and resid 2120 through 2124 Processing sheet with id=AD6, first strand: chain 'A' and resid 2160 through 2164 Processing sheet with id=AD7, first strand: chain 'A' and resid 2190 through 2194 Processing sheet with id=AD8, first strand: chain 'A' and resid 2210 through 2213 Processing sheet with id=AD9, first strand: chain 'A' and resid 2234 through 2238 Processing sheet with id=AE1, first strand: chain 'A' and resid 2254 through 2258 Processing sheet with id=AE2, first strand: chain 'A' and resid 2274 through 2278 Processing sheet with id=AE3, first strand: chain 'A' and resid 2294 through 2298 Processing sheet with id=AE4, first strand: chain 'A' and resid 2327 through 2328 822 hydrogen bonds defined for protein. 2199 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.89 Time building geometry restraints manager: 5.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6204 1.34 - 1.46: 3930 1.46 - 1.57: 9147 1.57 - 1.69: 0 1.69 - 1.81: 97 Bond restraints: 19378 Sorted by residual: bond pdb=" CG LEU A2311 " pdb=" CD2 LEU A2311 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.32e+00 bond pdb=" CB TRP A1264 " pdb=" CG TRP A1264 " ideal model delta sigma weight residual 1.498 1.470 0.028 3.10e-02 1.04e+03 8.08e-01 bond pdb=" CB ILE A 965 " pdb=" CG2 ILE A 965 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.03e-01 bond pdb=" N GLU A 574 " pdb=" CA GLU A 574 " ideal model delta sigma weight residual 1.452 1.463 -0.011 1.30e-02 5.92e+03 7.62e-01 bond pdb=" CG GLN A 835 " pdb=" CD GLN A 835 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 6.97e-01 ... (remaining 19373 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 25766 1.64 - 3.27: 402 3.27 - 4.91: 54 4.91 - 6.54: 9 6.54 - 8.18: 2 Bond angle restraints: 26233 Sorted by residual: angle pdb=" C GLU A1961 " pdb=" N THR A1962 " pdb=" CA THR A1962 " ideal model delta sigma weight residual 121.54 127.77 -6.23 1.91e+00 2.74e-01 1.06e+01 angle pdb=" C GLU A1947 " pdb=" N TRP A1948 " pdb=" CA TRP A1948 " ideal model delta sigma weight residual 122.56 117.80 4.76 1.50e+00 4.44e-01 1.01e+01 angle pdb=" C HIS A1186 " pdb=" N PHE A1187 " pdb=" CA PHE A1187 " ideal model delta sigma weight residual 122.20 127.27 -5.07 1.72e+00 3.38e-01 8.70e+00 angle pdb=" C THR A1179 " pdb=" N VAL A1180 " pdb=" CA VAL A1180 " ideal model delta sigma weight residual 123.16 120.09 3.07 1.06e+00 8.90e-01 8.36e+00 angle pdb=" N HIS A1186 " pdb=" CA HIS A1186 " pdb=" C HIS A1186 " ideal model delta sigma weight residual 110.80 116.44 -5.64 2.13e+00 2.20e-01 7.01e+00 ... (remaining 26228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 11017 17.44 - 34.89: 436 34.89 - 52.33: 94 52.33 - 69.78: 24 69.78 - 87.22: 6 Dihedral angle restraints: 11577 sinusoidal: 4629 harmonic: 6948 Sorted by residual: dihedral pdb=" CA ASP A1037 " pdb=" C ASP A1037 " pdb=" N GLY A1038 " pdb=" CA GLY A1038 " ideal model delta harmonic sigma weight residual -180.00 -146.95 -33.05 0 5.00e+00 4.00e-02 4.37e+01 dihedral pdb=" CA LEU A1113 " pdb=" C LEU A1113 " pdb=" N ARG A1114 " pdb=" CA ARG A1114 " ideal model delta harmonic sigma weight residual -180.00 -154.18 -25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA TYR A 577 " pdb=" C TYR A 577 " pdb=" N ILE A 578 " pdb=" CA ILE A 578 " ideal model delta harmonic sigma weight residual 180.00 154.97 25.03 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 11574 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1803 0.034 - 0.068: 736 0.068 - 0.102: 225 0.102 - 0.136: 133 0.136 - 0.170: 8 Chirality restraints: 2905 Sorted by residual: chirality pdb=" CA HIS A1186 " pdb=" N HIS A1186 " pdb=" C HIS A1186 " pdb=" CB HIS A1186 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA ILE A 578 " pdb=" N ILE A 578 " pdb=" C ILE A 578 " pdb=" CB ILE A 578 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CB ILE A 646 " pdb=" CA ILE A 646 " pdb=" CG1 ILE A 646 " pdb=" CG2 ILE A 646 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 2902 not shown) Planarity restraints: 3412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 924 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C HIS A 924 " 0.032 2.00e-02 2.50e+03 pdb=" O HIS A 924 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE A 925 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 926 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.37e+00 pdb=" C THR A 926 " -0.032 2.00e-02 2.50e+03 pdb=" O THR A 926 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU A 927 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 643 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO A 644 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 644 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 644 " -0.022 5.00e-02 4.00e+02 ... (remaining 3409 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 353 2.67 - 3.23: 18372 3.23 - 3.79: 29475 3.79 - 4.34: 42067 4.34 - 4.90: 68261 Nonbonded interactions: 158528 Sorted by model distance: nonbonded pdb=" OH TYR A1645 " pdb=" O ASN A1675 " model vdw 2.118 3.040 nonbonded pdb=" OD2 ASP A 270 " pdb=" OG SER A 469 " model vdw 2.161 3.040 nonbonded pdb=" OH TYR A1508 " pdb=" O ASP A1546 " model vdw 2.170 3.040 nonbonded pdb=" O GLY A1431 " pdb=" OH TYR A1462 " model vdw 2.191 3.040 nonbonded pdb=" O VAL A 373 " pdb=" OH TYR A 478 " model vdw 2.212 3.040 ... (remaining 158523 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 11.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 59.450 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.277 19381 Z= 0.185 Angle : 0.542 8.176 26233 Z= 0.307 Chirality : 0.045 0.170 2905 Planarity : 0.003 0.040 3412 Dihedral : 10.634 87.222 7125 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.00 % Favored : 94.88 % Rotamer: Outliers : 2.20 % Allowed : 3.28 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2361 helix: 1.49 (0.21), residues: 647 sheet: -0.30 (0.24), residues: 450 loop : -0.32 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1232 HIS 0.003 0.001 HIS A2016 PHE 0.017 0.002 PHE A1638 TYR 0.017 0.001 TYR A1648 ARG 0.003 0.000 ARG A1265 Details of bonding type rmsd hydrogen bonds : bond 0.12333 ( 820) hydrogen bonds : angle 6.77426 ( 2199) metal coordination : bond 0.22299 ( 3) covalent geometry : bond 0.00350 (19378) covalent geometry : angle 0.54209 (26233) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 450 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.7707 (tpt) cc_final: 0.7404 (tpt) REVERT: A 273 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7650 (ptp-170) REVERT: A 329 GLU cc_start: 0.5064 (OUTLIER) cc_final: 0.4699 (pp20) REVERT: A 493 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8313 (tp) REVERT: A 580 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7459 (m-80) REVERT: A 700 MET cc_start: 0.7857 (mmm) cc_final: 0.7569 (mmp) REVERT: A 830 SER cc_start: 0.8504 (t) cc_final: 0.8184 (m) REVERT: A 1139 LEU cc_start: 0.8450 (mt) cc_final: 0.8078 (mt) REVERT: A 1185 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.5380 (p0) REVERT: A 1232 TRP cc_start: 0.8221 (p-90) cc_final: 0.7812 (p-90) REVERT: A 1347 ASP cc_start: 0.7598 (t0) cc_final: 0.7281 (t0) REVERT: A 1655 MET cc_start: 0.7410 (tpp) cc_final: 0.6966 (ttm) REVERT: A 1768 VAL cc_start: 0.8925 (m) cc_final: 0.8667 (t) REVERT: A 1790 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8362 (m) REVERT: A 2162 PHE cc_start: 0.5789 (m-80) cc_final: 0.5414 (m-80) REVERT: A 2250 ILE cc_start: 0.7363 (mt) cc_final: 0.6987 (mt) REVERT: A 2260 ASN cc_start: 0.8389 (m110) cc_final: 0.7824 (t0) REVERT: A 2271 MET cc_start: 0.8130 (ttm) cc_final: 0.7680 (ttm) REVERT: A 2313 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.6032 (pt0) outliers start: 47 outliers final: 12 residues processed: 486 average time/residue: 0.3417 time to fit residues: 252.8929 Evaluate side-chains 253 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 234 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1185 ASP Chi-restraints excluded: chain A residue 1638 PHE Chi-restraints excluded: chain A residue 1648 TYR Chi-restraints excluded: chain A residue 1748 ASP Chi-restraints excluded: chain A residue 1790 VAL Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1859 VAL Chi-restraints excluded: chain A residue 2313 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 184 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 214 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 579 HIS A 596 ASN A 659 ASN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1387 HIS A1439 ASN A1444 GLN A1570 ASN A1651 ASN A2016 HIS A2026 GLN ** A2272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2309 ASN ** A2314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.106891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.091794 restraints weight = 39357.751| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.02 r_work: 0.3320 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19381 Z= 0.141 Angle : 0.560 9.164 26233 Z= 0.307 Chirality : 0.046 0.163 2905 Planarity : 0.004 0.058 3412 Dihedral : 5.972 56.729 2585 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.04 % Favored : 94.83 % Rotamer: Outliers : 2.20 % Allowed : 9.42 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.18), residues: 2361 helix: 1.82 (0.20), residues: 652 sheet: -0.17 (0.24), residues: 436 loop : -0.40 (0.18), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1344 HIS 0.003 0.001 HIS A 35 PHE 0.034 0.001 PHE A1188 TYR 0.027 0.002 TYR A 921 ARG 0.006 0.000 ARG A 751 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 820) hydrogen bonds : angle 5.20241 ( 2199) metal coordination : bond 0.00186 ( 3) covalent geometry : bond 0.00313 (19378) covalent geometry : angle 0.56035 (26233) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 265 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.6786 (m-30) cc_final: 0.6565 (m-30) REVERT: A 176 MET cc_start: 0.7958 (tpt) cc_final: 0.7498 (tpt) REVERT: A 229 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7541 (tt) REVERT: A 516 MET cc_start: 0.8163 (tmm) cc_final: 0.7912 (ttp) REVERT: A 580 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7816 (m-80) REVERT: A 700 MET cc_start: 0.8301 (mmm) cc_final: 0.8081 (mmt) REVERT: A 727 MET cc_start: 0.7304 (mmm) cc_final: 0.7035 (mmm) REVERT: A 830 SER cc_start: 0.8906 (t) cc_final: 0.8429 (m) REVERT: A 929 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8201 (mm) REVERT: A 1032 ILE cc_start: 0.8662 (mt) cc_final: 0.8443 (mm) REVERT: A 1220 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8496 (ttp) REVERT: A 1232 TRP cc_start: 0.8342 (p-90) cc_final: 0.8111 (p-90) REVERT: A 1332 MET cc_start: 0.8311 (ttm) cc_final: 0.7829 (ttm) REVERT: A 1347 ASP cc_start: 0.8531 (t0) cc_final: 0.8283 (t0) REVERT: A 1434 LYS cc_start: 0.8063 (mppt) cc_final: 0.7819 (mtmt) REVERT: A 1569 MET cc_start: 0.7721 (mmt) cc_final: 0.7509 (mmt) REVERT: A 1655 MET cc_start: 0.7796 (tpp) cc_final: 0.7112 (ttp) REVERT: A 1925 PHE cc_start: 0.5840 (t80) cc_final: 0.5502 (t80) REVERT: A 2025 MET cc_start: 0.7193 (ttp) cc_final: 0.6780 (ttt) REVERT: A 2088 TYR cc_start: 0.6349 (m-80) cc_final: 0.5889 (m-80) REVERT: A 2271 MET cc_start: 0.8461 (ttm) cc_final: 0.8239 (ttm) REVERT: A 2280 ASP cc_start: 0.7600 (t70) cc_final: 0.7278 (t70) REVERT: A 2328 LEU cc_start: 0.7510 (mt) cc_final: 0.7234 (mt) outliers start: 47 outliers final: 20 residues processed: 299 average time/residue: 0.3525 time to fit residues: 165.8025 Evaluate side-chains 231 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1220 MET Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1587 SER Chi-restraints excluded: chain A residue 1638 PHE Chi-restraints excluded: chain A residue 1648 TYR Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1862 ASP Chi-restraints excluded: chain A residue 1955 MET Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain A residue 2072 SER Chi-restraints excluded: chain A residue 2147 ASN Chi-restraints excluded: chain A residue 2282 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 172 optimal weight: 0.7980 chunk 143 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 191 optimal weight: 0.0470 chunk 43 optimal weight: 1.9990 chunk 229 optimal weight: 0.9990 chunk 215 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 HIS A 659 ASN A1651 ASN A1934 ASN ** A1971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2272 GLN ** A2314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.107507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.092509 restraints weight = 39188.687| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.01 r_work: 0.3331 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19381 Z= 0.114 Angle : 0.525 9.049 26233 Z= 0.287 Chirality : 0.045 0.153 2905 Planarity : 0.003 0.052 3412 Dihedral : 5.145 54.322 2560 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.74 % Favored : 95.13 % Rotamer: Outliers : 2.58 % Allowed : 10.12 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.18), residues: 2361 helix: 2.01 (0.20), residues: 655 sheet: -0.30 (0.23), residues: 477 loop : -0.38 (0.19), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1264 HIS 0.005 0.001 HIS A1126 PHE 0.034 0.001 PHE A1188 TYR 0.022 0.001 TYR A2089 ARG 0.002 0.000 ARG A1057 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 820) hydrogen bonds : angle 4.90073 ( 2199) metal coordination : bond 0.00166 ( 3) covalent geometry : bond 0.00251 (19378) covalent geometry : angle 0.52463 (26233) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 226 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.8013 (OUTLIER) cc_final: 0.7748 (t) REVERT: A 176 MET cc_start: 0.7920 (tpt) cc_final: 0.7295 (tpt) REVERT: A 229 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7524 (tt) REVERT: A 448 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7219 (mmm) REVERT: A 516 MET cc_start: 0.8094 (tmm) cc_final: 0.7782 (ttp) REVERT: A 581 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7716 (mm) REVERT: A 648 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.7018 (tp) REVERT: A 727 MET cc_start: 0.7280 (mmm) cc_final: 0.6923 (mmm) REVERT: A 830 SER cc_start: 0.8957 (t) cc_final: 0.8527 (m) REVERT: A 1144 MET cc_start: 0.8220 (ttm) cc_final: 0.7895 (ttp) REVERT: A 1232 TRP cc_start: 0.8347 (p-90) cc_final: 0.8023 (p-90) REVERT: A 1347 ASP cc_start: 0.8530 (t0) cc_final: 0.8246 (t0) REVERT: A 1655 MET cc_start: 0.7666 (tpp) cc_final: 0.7018 (ttp) REVERT: A 1739 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8182 (ptm-80) REVERT: A 1882 ASP cc_start: 0.7400 (t0) cc_final: 0.6959 (t0) REVERT: A 2025 MET cc_start: 0.6979 (ttp) cc_final: 0.6765 (ttt) REVERT: A 2271 MET cc_start: 0.8384 (ttm) cc_final: 0.8158 (ttm) REVERT: A 2280 ASP cc_start: 0.7599 (t70) cc_final: 0.7382 (t70) outliers start: 55 outliers final: 30 residues processed: 265 average time/residue: 0.3446 time to fit residues: 143.9418 Evaluate side-chains 223 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1183 ASP Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1643 THR Chi-restraints excluded: chain A residue 1648 TYR Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1739 ARG Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1862 ASP Chi-restraints excluded: chain A residue 1880 ILE Chi-restraints excluded: chain A residue 1955 MET Chi-restraints excluded: chain A residue 1966 PHE Chi-restraints excluded: chain A residue 2005 MET Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain A residue 2320 ILE Chi-restraints excluded: chain A residue 2326 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 214 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 221 optimal weight: 0.0980 chunk 148 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN A 579 HIS A 596 ASN A 659 ASN A1651 ASN ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.107428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.092452 restraints weight = 39438.198| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.03 r_work: 0.3328 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19381 Z= 0.114 Angle : 0.512 10.386 26233 Z= 0.278 Chirality : 0.044 0.152 2905 Planarity : 0.003 0.050 3412 Dihedral : 4.886 46.718 2556 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.08 % Favored : 94.79 % Rotamer: Outliers : 2.91 % Allowed : 10.78 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.18), residues: 2361 helix: 2.04 (0.20), residues: 660 sheet: -0.27 (0.24), residues: 468 loop : -0.44 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1344 HIS 0.005 0.001 HIS A1126 PHE 0.015 0.001 PHE A1638 TYR 0.020 0.001 TYR A 742 ARG 0.004 0.000 ARG A 751 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 820) hydrogen bonds : angle 4.76653 ( 2199) metal coordination : bond 0.00229 ( 3) covalent geometry : bond 0.00250 (19378) covalent geometry : angle 0.51160 (26233) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 217 time to evaluate : 4.164 Fit side-chains revert: symmetry clash REVERT: A 83 VAL cc_start: 0.8023 (OUTLIER) cc_final: 0.7749 (t) REVERT: A 176 MET cc_start: 0.7914 (tpt) cc_final: 0.7297 (tpt) REVERT: A 229 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7511 (tt) REVERT: A 448 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7382 (mmm) REVERT: A 516 MET cc_start: 0.8095 (tmm) cc_final: 0.7769 (ttp) REVERT: A 648 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7042 (tp) REVERT: A 830 SER cc_start: 0.8968 (t) cc_final: 0.8514 (m) REVERT: A 833 ASP cc_start: 0.7495 (m-30) cc_final: 0.7128 (m-30) REVERT: A 845 LYS cc_start: 0.8444 (mmtt) cc_final: 0.8198 (mmtt) REVERT: A 1032 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8183 (mt) REVERT: A 1141 ASP cc_start: 0.6185 (t0) cc_final: 0.5756 (t0) REVERT: A 1144 MET cc_start: 0.8195 (ttm) cc_final: 0.7843 (ttp) REVERT: A 1232 TRP cc_start: 0.8434 (p-90) cc_final: 0.8138 (p-90) REVERT: A 1347 ASP cc_start: 0.8520 (t0) cc_final: 0.8251 (t0) REVERT: A 1588 MET cc_start: 0.7570 (mmp) cc_final: 0.7214 (mmp) REVERT: A 1655 MET cc_start: 0.7660 (tpp) cc_final: 0.7029 (ttp) REVERT: A 1739 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8245 (ptm-80) REVERT: A 1994 ASP cc_start: 0.6838 (m-30) cc_final: 0.6634 (m-30) REVERT: A 2025 MET cc_start: 0.6974 (ttp) cc_final: 0.6667 (ttt) REVERT: A 2184 GLN cc_start: 0.7823 (tt0) cc_final: 0.7291 (tt0) REVERT: A 2271 MET cc_start: 0.8330 (ttm) cc_final: 0.8123 (ttm) REVERT: A 2282 MET cc_start: 0.7758 (mmt) cc_final: 0.6894 (mmt) REVERT: A 2302 PHE cc_start: 0.6939 (OUTLIER) cc_final: 0.6058 (t80) outliers start: 62 outliers final: 40 residues processed: 256 average time/residue: 0.4650 time to fit residues: 194.2006 Evaluate side-chains 237 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1183 ASP Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1587 SER Chi-restraints excluded: chain A residue 1611 ILE Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1643 THR Chi-restraints excluded: chain A residue 1648 TYR Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1739 ARG Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1859 VAL Chi-restraints excluded: chain A residue 1862 ASP Chi-restraints excluded: chain A residue 1955 MET Chi-restraints excluded: chain A residue 2005 MET Chi-restraints excluded: chain A residue 2011 GLU Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain A residue 2192 VAL Chi-restraints excluded: chain A residue 2302 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 185 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 224 optimal weight: 0.6980 chunk 111 optimal weight: 0.0870 chunk 46 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 32 optimal weight: 0.3980 chunk 195 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 HIS A1651 ASN ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2314 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 = 0.3687 r_free = 0.3687 target = 0.107782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.092808 restraints weight = 39632.489| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.03 r_work: 0.3337 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19381 Z= 0.107 Angle : 0.502 10.498 26233 Z= 0.272 Chirality : 0.044 0.176 2905 Planarity : 0.003 0.051 3412 Dihedral : 4.794 46.107 2556 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.12 % Favored : 94.75 % Rotamer: Outliers : 2.53 % Allowed : 12.23 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 2361 helix: 2.13 (0.20), residues: 660 sheet: -0.19 (0.23), residues: 477 loop : -0.52 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1264 HIS 0.004 0.001 HIS A1126 PHE 0.044 0.001 PHE A1188 TYR 0.023 0.001 TYR A2089 ARG 0.004 0.000 ARG A1057 Details of bonding type rmsd hydrogen bonds : bond 0.03294 ( 820) hydrogen bonds : angle 4.66228 ( 2199) metal coordination : bond 0.00139 ( 3) covalent geometry : bond 0.00233 (19378) covalent geometry : angle 0.50192 (26233) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 218 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.8021 (OUTLIER) cc_final: 0.7754 (t) REVERT: A 176 MET cc_start: 0.7893 (tpt) cc_final: 0.7274 (tpt) REVERT: A 229 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7529 (tt) REVERT: A 436 MET cc_start: 0.7894 (mmm) cc_final: 0.7641 (mmm) REVERT: A 516 MET cc_start: 0.8055 (tmm) cc_final: 0.7732 (ttp) REVERT: A 581 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7535 (mt) REVERT: A 648 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.7030 (tp) REVERT: A 727 MET cc_start: 0.7403 (mmm) cc_final: 0.6816 (mmm) REVERT: A 751 ARG cc_start: 0.8344 (mmm-85) cc_final: 0.7875 (mmm-85) REVERT: A 830 SER cc_start: 0.8974 (t) cc_final: 0.8558 (m) REVERT: A 1032 ILE cc_start: 0.8513 (mm) cc_final: 0.8224 (mt) REVERT: A 1144 MET cc_start: 0.8175 (ttm) cc_final: 0.7828 (ttp) REVERT: A 1232 TRP cc_start: 0.8418 (p-90) cc_final: 0.8102 (p-90) REVERT: A 1347 ASP cc_start: 0.8506 (t0) cc_final: 0.8232 (t0) REVERT: A 1462 TYR cc_start: 0.7581 (t80) cc_final: 0.7154 (t80) REVERT: A 1471 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7378 (mp0) REVERT: A 1655 MET cc_start: 0.7658 (tpp) cc_final: 0.7036 (ttp) REVERT: A 1881 ILE cc_start: 0.6776 (mp) cc_final: 0.6463 (mt) REVERT: A 2169 LYS cc_start: 0.7985 (mtpt) cc_final: 0.7650 (mtpp) REVERT: A 2184 GLN cc_start: 0.7830 (tt0) cc_final: 0.7199 (tt0) REVERT: A 2271 MET cc_start: 0.8277 (ttm) cc_final: 0.8045 (ttm) REVERT: A 2280 ASP cc_start: 0.8060 (p0) cc_final: 0.7831 (p0) REVERT: A 2282 MET cc_start: 0.7984 (mmt) cc_final: 0.7056 (mmt) REVERT: A 2302 PHE cc_start: 0.6756 (OUTLIER) cc_final: 0.5749 (t80) outliers start: 54 outliers final: 35 residues processed: 251 average time/residue: 0.3369 time to fit residues: 137.4276 Evaluate side-chains 228 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1183 ASP Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1587 SER Chi-restraints excluded: chain A residue 1611 ILE Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1643 THR Chi-restraints excluded: chain A residue 1648 TYR Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1859 VAL Chi-restraints excluded: chain A residue 1862 ASP Chi-restraints excluded: chain A residue 2192 VAL Chi-restraints excluded: chain A residue 2302 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 81 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 232 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 123 optimal weight: 0.3980 chunk 35 optimal weight: 0.0470 chunk 7 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 402 GLN A 579 HIS A1070 ASN ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1651 ASN ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2292 GLN ** A2314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.104923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.089870 restraints weight = 39836.648| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.02 r_work: 0.3282 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19381 Z= 0.170 Angle : 0.553 10.225 26233 Z= 0.299 Chirality : 0.046 0.184 2905 Planarity : 0.003 0.050 3412 Dihedral : 5.049 45.955 2556 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.72 % Favored : 94.16 % Rotamer: Outliers : 3.05 % Allowed : 12.93 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.17), residues: 2361 helix: 1.82 (0.20), residues: 668 sheet: -0.31 (0.24), residues: 447 loop : -0.64 (0.18), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1264 HIS 0.004 0.001 HIS A1186 PHE 0.043 0.002 PHE A1188 TYR 0.020 0.002 TYR A 742 ARG 0.003 0.000 ARG A 751 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 820) hydrogen bonds : angle 4.85239 ( 2199) metal coordination : bond 0.00385 ( 3) covalent geometry : bond 0.00395 (19378) covalent geometry : angle 0.55269 (26233) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 196 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.7972 (tpt) cc_final: 0.7531 (tpt) REVERT: A 229 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7647 (tt) REVERT: A 489 MET cc_start: 0.8832 (mmt) cc_final: 0.8481 (mmt) REVERT: A 516 MET cc_start: 0.8111 (tmm) cc_final: 0.7801 (ttp) REVERT: A 567 SER cc_start: 0.7552 (OUTLIER) cc_final: 0.7197 (t) REVERT: A 727 MET cc_start: 0.7487 (mmm) cc_final: 0.6914 (mmm) REVERT: A 1032 ILE cc_start: 0.8529 (mm) cc_final: 0.8226 (mt) REVERT: A 1141 ASP cc_start: 0.6089 (t0) cc_final: 0.5202 (t0) REVERT: A 1144 MET cc_start: 0.8229 (ttm) cc_final: 0.7882 (ttp) REVERT: A 1232 TRP cc_start: 0.8520 (p-90) cc_final: 0.8247 (p-90) REVERT: A 1347 ASP cc_start: 0.8514 (t0) cc_final: 0.8251 (t0) REVERT: A 1462 TYR cc_start: 0.7823 (t80) cc_final: 0.7551 (t80) REVERT: A 1471 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7247 (mp0) REVERT: A 1655 MET cc_start: 0.7831 (tpp) cc_final: 0.7237 (ttp) REVERT: A 2069 PHE cc_start: 0.6259 (m-80) cc_final: 0.5923 (m-80) REVERT: A 2169 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7707 (mtpp) REVERT: A 2184 GLN cc_start: 0.7773 (tt0) cc_final: 0.7242 (tt0) REVERT: A 2271 MET cc_start: 0.8343 (ttm) cc_final: 0.8116 (ttm) REVERT: A 2282 MET cc_start: 0.7989 (mmt) cc_final: 0.7310 (mmt) REVERT: A 2302 PHE cc_start: 0.6738 (OUTLIER) cc_final: 0.5896 (t80) REVERT: A 2346 VAL cc_start: 0.2213 (OUTLIER) cc_final: 0.1361 (p) outliers start: 65 outliers final: 47 residues processed: 242 average time/residue: 0.3268 time to fit residues: 128.0530 Evaluate side-chains 233 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 182 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1183 ASP Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1499 MET Chi-restraints excluded: chain A residue 1565 ILE Chi-restraints excluded: chain A residue 1587 SER Chi-restraints excluded: chain A residue 1611 ILE Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1643 THR Chi-restraints excluded: chain A residue 1648 TYR Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1725 ILE Chi-restraints excluded: chain A residue 1735 ASP Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1859 VAL Chi-restraints excluded: chain A residue 1862 ASP Chi-restraints excluded: chain A residue 2005 MET Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain A residue 2147 ASN Chi-restraints excluded: chain A residue 2192 VAL Chi-restraints excluded: chain A residue 2302 PHE Chi-restraints excluded: chain A residue 2346 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 155 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 110 optimal weight: 0.0970 chunk 43 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 166 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1997 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.106737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.091756 restraints weight = 39354.826| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.02 r_work: 0.3315 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19381 Z= 0.113 Angle : 0.517 11.507 26233 Z= 0.279 Chirality : 0.044 0.178 2905 Planarity : 0.003 0.048 3412 Dihedral : 4.875 46.301 2556 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.12 % Favored : 94.75 % Rotamer: Outliers : 2.48 % Allowed : 13.45 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.18), residues: 2361 helix: 2.07 (0.20), residues: 663 sheet: -0.32 (0.24), residues: 465 loop : -0.57 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 118 HIS 0.004 0.001 HIS A1186 PHE 0.046 0.001 PHE A1188 TYR 0.023 0.001 TYR A2170 ARG 0.003 0.000 ARG A 751 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 820) hydrogen bonds : angle 4.68504 ( 2199) metal coordination : bond 0.00184 ( 3) covalent geometry : bond 0.00250 (19378) covalent geometry : angle 0.51683 (26233) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 200 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7998 (OUTLIER) cc_final: 0.7714 (t) REVERT: A 176 MET cc_start: 0.7912 (tpt) cc_final: 0.7307 (tpt) REVERT: A 229 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7573 (tt) REVERT: A 438 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7212 (mm-30) REVERT: A 489 MET cc_start: 0.8822 (mmt) cc_final: 0.8447 (mmt) REVERT: A 516 MET cc_start: 0.8116 (tmm) cc_final: 0.7773 (ttp) REVERT: A 581 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7639 (mt) REVERT: A 727 MET cc_start: 0.7540 (mmm) cc_final: 0.6892 (mmm) REVERT: A 751 ARG cc_start: 0.8245 (mmm-85) cc_final: 0.7695 (mmm-85) REVERT: A 830 SER cc_start: 0.9003 (t) cc_final: 0.8553 (m) REVERT: A 1032 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8251 (mt) REVERT: A 1099 ILE cc_start: 0.6745 (tt) cc_final: 0.6092 (mm) REVERT: A 1144 MET cc_start: 0.8225 (ttm) cc_final: 0.7884 (ttp) REVERT: A 1232 TRP cc_start: 0.8480 (p-90) cc_final: 0.8202 (p-90) REVERT: A 1312 LEU cc_start: 0.7977 (mm) cc_final: 0.7718 (mt) REVERT: A 1347 ASP cc_start: 0.8486 (t0) cc_final: 0.8200 (t0) REVERT: A 1462 TYR cc_start: 0.7733 (t80) cc_final: 0.7445 (t80) REVERT: A 1471 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7253 (mp0) REVERT: A 1655 MET cc_start: 0.7816 (tpp) cc_final: 0.7161 (ttp) REVERT: A 1666 SER cc_start: 0.9126 (m) cc_final: 0.8866 (t) REVERT: A 2069 PHE cc_start: 0.6293 (m-80) cc_final: 0.6004 (m-80) REVERT: A 2169 LYS cc_start: 0.8233 (mtpt) cc_final: 0.7860 (mttm) REVERT: A 2184 GLN cc_start: 0.7745 (tt0) cc_final: 0.7243 (tt0) REVERT: A 2212 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.7979 (pp) REVERT: A 2271 MET cc_start: 0.8244 (ttm) cc_final: 0.7982 (ttm) REVERT: A 2280 ASP cc_start: 0.7927 (p0) cc_final: 0.7653 (p0) REVERT: A 2282 MET cc_start: 0.7989 (mmt) cc_final: 0.7637 (mmt) REVERT: A 2302 PHE cc_start: 0.6658 (OUTLIER) cc_final: 0.5784 (t80) REVERT: A 2346 VAL cc_start: 0.2253 (OUTLIER) cc_final: 0.1397 (p) outliers start: 53 outliers final: 38 residues processed: 235 average time/residue: 0.3083 time to fit residues: 116.3140 Evaluate side-chains 228 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 183 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1517 LYS Chi-restraints excluded: chain A residue 1587 SER Chi-restraints excluded: chain A residue 1611 ILE Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1643 THR Chi-restraints excluded: chain A residue 1648 TYR Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1735 ASP Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1859 VAL Chi-restraints excluded: chain A residue 1862 ASP Chi-restraints excluded: chain A residue 1875 SER Chi-restraints excluded: chain A residue 2005 MET Chi-restraints excluded: chain A residue 2147 ASN Chi-restraints excluded: chain A residue 2192 VAL Chi-restraints excluded: chain A residue 2212 ILE Chi-restraints excluded: chain A residue 2302 PHE Chi-restraints excluded: chain A residue 2346 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 111 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 195 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 HIS ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1651 ASN ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1971 GLN ** A1997 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.105307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.090208 restraints weight = 39679.766| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.03 r_work: 0.3286 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19381 Z= 0.148 Angle : 0.545 13.238 26233 Z= 0.293 Chirality : 0.045 0.174 2905 Planarity : 0.003 0.048 3412 Dihedral : 4.994 45.912 2556 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.80 % Favored : 94.07 % Rotamer: Outliers : 2.53 % Allowed : 14.10 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.17), residues: 2361 helix: 1.89 (0.20), residues: 668 sheet: -0.32 (0.24), residues: 465 loop : -0.70 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1264 HIS 0.003 0.001 HIS A1186 PHE 0.020 0.001 PHE A1269 TYR 0.022 0.001 TYR A 742 ARG 0.003 0.000 ARG A1739 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 820) hydrogen bonds : angle 4.76865 ( 2199) metal coordination : bond 0.00308 ( 3) covalent geometry : bond 0.00341 (19378) covalent geometry : angle 0.54477 (26233) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 200 time to evaluate : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.7930 (tpt) cc_final: 0.7497 (tpt) REVERT: A 229 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7626 (tt) REVERT: A 438 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7358 (mm-30) REVERT: A 489 MET cc_start: 0.8826 (mmt) cc_final: 0.8368 (mmt) REVERT: A 516 MET cc_start: 0.8181 (tmm) cc_final: 0.7856 (ttp) REVERT: A 567 SER cc_start: 0.7541 (OUTLIER) cc_final: 0.7222 (t) REVERT: A 727 MET cc_start: 0.7597 (mmm) cc_final: 0.7029 (mmm) REVERT: A 751 ARG cc_start: 0.8298 (mmm-85) cc_final: 0.7692 (mmm-85) REVERT: A 830 SER cc_start: 0.9014 (t) cc_final: 0.8567 (m) REVERT: A 845 LYS cc_start: 0.7897 (mptt) cc_final: 0.7640 (mmtt) REVERT: A 1032 ILE cc_start: 0.8488 (mm) cc_final: 0.8218 (mt) REVERT: A 1099 ILE cc_start: 0.6794 (tt) cc_final: 0.6036 (mm) REVERT: A 1144 MET cc_start: 0.8214 (ttm) cc_final: 0.7948 (ttp) REVERT: A 1182 ASP cc_start: 0.7089 (m-30) cc_final: 0.6151 (t0) REVERT: A 1232 TRP cc_start: 0.8531 (p-90) cc_final: 0.8274 (p-90) REVERT: A 1312 LEU cc_start: 0.8000 (mm) cc_final: 0.7798 (mt) REVERT: A 1347 ASP cc_start: 0.8486 (t0) cc_final: 0.8200 (t0) REVERT: A 1371 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.7833 (pt) REVERT: A 1462 TYR cc_start: 0.7819 (t80) cc_final: 0.7593 (t80) REVERT: A 1471 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7255 (mp0) REVERT: A 1655 MET cc_start: 0.7837 (tpp) cc_final: 0.7196 (ttp) REVERT: A 1666 SER cc_start: 0.9162 (m) cc_final: 0.8917 (t) REVERT: A 2069 PHE cc_start: 0.6353 (m-80) cc_final: 0.6048 (m-80) REVERT: A 2169 LYS cc_start: 0.8300 (mtpt) cc_final: 0.7932 (mttm) REVERT: A 2184 GLN cc_start: 0.7796 (tt0) cc_final: 0.7324 (tt0) REVERT: A 2212 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.7972 (pp) REVERT: A 2271 MET cc_start: 0.8308 (ttm) cc_final: 0.8054 (ttm) REVERT: A 2280 ASP cc_start: 0.7929 (p0) cc_final: 0.7699 (p0) REVERT: A 2282 MET cc_start: 0.8089 (mmt) cc_final: 0.7701 (mmt) REVERT: A 2302 PHE cc_start: 0.6799 (OUTLIER) cc_final: 0.5940 (t80) REVERT: A 2346 VAL cc_start: 0.2446 (OUTLIER) cc_final: 0.1688 (p) outliers start: 54 outliers final: 45 residues processed: 235 average time/residue: 0.2878 time to fit residues: 109.8653 Evaluate side-chains 238 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 187 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1499 MET Chi-restraints excluded: chain A residue 1517 LYS Chi-restraints excluded: chain A residue 1565 ILE Chi-restraints excluded: chain A residue 1587 SER Chi-restraints excluded: chain A residue 1611 ILE Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1643 THR Chi-restraints excluded: chain A residue 1648 TYR Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1725 ILE Chi-restraints excluded: chain A residue 1735 ASP Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1859 VAL Chi-restraints excluded: chain A residue 1862 ASP Chi-restraints excluded: chain A residue 1875 SER Chi-restraints excluded: chain A residue 2005 MET Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain A residue 2147 ASN Chi-restraints excluded: chain A residue 2192 VAL Chi-restraints excluded: chain A residue 2212 ILE Chi-restraints excluded: chain A residue 2302 PHE Chi-restraints excluded: chain A residue 2311 LEU Chi-restraints excluded: chain A residue 2346 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 51 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 chunk 211 optimal weight: 6.9990 chunk 221 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN A 579 HIS ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1941 ASN A2260 ASN ** A2314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.105056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.089954 restraints weight = 39821.994| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.03 r_work: 0.3282 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19381 Z= 0.152 Angle : 0.552 12.440 26233 Z= 0.296 Chirality : 0.046 0.191 2905 Planarity : 0.003 0.049 3412 Dihedral : 5.054 47.023 2556 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.76 % Favored : 94.11 % Rotamer: Outliers : 2.86 % Allowed : 14.25 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.17), residues: 2361 helix: 1.82 (0.20), residues: 670 sheet: -0.36 (0.23), residues: 475 loop : -0.76 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1264 HIS 0.004 0.001 HIS A1186 PHE 0.050 0.002 PHE A1188 TYR 0.024 0.001 TYR A 742 ARG 0.006 0.000 ARG A1057 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 820) hydrogen bonds : angle 4.79777 ( 2199) metal coordination : bond 0.00319 ( 3) covalent geometry : bond 0.00350 (19378) covalent geometry : angle 0.55163 (26233) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 193 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.7929 (tpt) cc_final: 0.7500 (tpt) REVERT: A 229 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7585 (tt) REVERT: A 329 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.6101 (pp20) REVERT: A 438 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7410 (mm-30) REVERT: A 516 MET cc_start: 0.8174 (tmm) cc_final: 0.7838 (ttp) REVERT: A 567 SER cc_start: 0.7588 (OUTLIER) cc_final: 0.6714 (m) REVERT: A 727 MET cc_start: 0.7584 (mmm) cc_final: 0.7019 (mmm) REVERT: A 751 ARG cc_start: 0.8277 (mmm-85) cc_final: 0.7659 (mmm-85) REVERT: A 830 SER cc_start: 0.9016 (t) cc_final: 0.8565 (m) REVERT: A 845 LYS cc_start: 0.7894 (mptt) cc_final: 0.7631 (mmtt) REVERT: A 1032 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8158 (mt) REVERT: A 1144 MET cc_start: 0.8230 (ttm) cc_final: 0.7966 (ttp) REVERT: A 1182 ASP cc_start: 0.7103 (m-30) cc_final: 0.6199 (t0) REVERT: A 1232 TRP cc_start: 0.8554 (p-90) cc_final: 0.8291 (p-90) REVERT: A 1312 LEU cc_start: 0.7991 (mm) cc_final: 0.7771 (mt) REVERT: A 1347 ASP cc_start: 0.8491 (t0) cc_final: 0.8235 (t0) REVERT: A 1371 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.7932 (pt) REVERT: A 1655 MET cc_start: 0.7786 (tpp) cc_final: 0.7081 (ttp) REVERT: A 1666 SER cc_start: 0.9161 (m) cc_final: 0.8931 (t) REVERT: A 2069 PHE cc_start: 0.6649 (m-80) cc_final: 0.6397 (m-80) REVERT: A 2169 LYS cc_start: 0.8295 (mtpt) cc_final: 0.7893 (mtpp) REVERT: A 2184 GLN cc_start: 0.7654 (tt0) cc_final: 0.7296 (tt0) REVERT: A 2212 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.7965 (pp) REVERT: A 2271 MET cc_start: 0.8331 (ttm) cc_final: 0.8081 (ttm) REVERT: A 2282 MET cc_start: 0.8067 (mmt) cc_final: 0.7683 (mmt) REVERT: A 2302 PHE cc_start: 0.6837 (OUTLIER) cc_final: 0.5933 (t80) REVERT: A 2346 VAL cc_start: 0.2533 (OUTLIER) cc_final: 0.2291 (t) outliers start: 61 outliers final: 45 residues processed: 234 average time/residue: 0.2908 time to fit residues: 110.1298 Evaluate side-chains 240 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 187 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1183 ASP Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1517 LYS Chi-restraints excluded: chain A residue 1587 SER Chi-restraints excluded: chain A residue 1611 ILE Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1643 THR Chi-restraints excluded: chain A residue 1648 TYR Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1725 ILE Chi-restraints excluded: chain A residue 1735 ASP Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1859 VAL Chi-restraints excluded: chain A residue 1862 ASP Chi-restraints excluded: chain A residue 1875 SER Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain A residue 2192 VAL Chi-restraints excluded: chain A residue 2212 ILE Chi-restraints excluded: chain A residue 2260 ASN Chi-restraints excluded: chain A residue 2302 PHE Chi-restraints excluded: chain A residue 2311 LEU Chi-restraints excluded: chain A residue 2346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 235 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 184 optimal weight: 0.0570 chunk 109 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 HIS ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1651 ASN A1917 ASN A1941 ASN ** A1997 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2260 ASN ** A2314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.106923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.091889 restraints weight = 39420.277| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.02 r_work: 0.3319 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19381 Z= 0.109 Angle : 0.523 12.676 26233 Z= 0.282 Chirality : 0.044 0.203 2905 Planarity : 0.003 0.048 3412 Dihedral : 4.858 46.723 2556 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.51 % Favored : 94.37 % Rotamer: Outliers : 2.44 % Allowed : 14.71 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.18), residues: 2361 helix: 2.13 (0.20), residues: 661 sheet: -0.30 (0.24), residues: 465 loop : -0.72 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1264 HIS 0.004 0.001 HIS A1186 PHE 0.054 0.001 PHE A1188 TYR 0.020 0.001 TYR A 742 ARG 0.004 0.000 ARG A1057 Details of bonding type rmsd hydrogen bonds : bond 0.03318 ( 820) hydrogen bonds : angle 4.65319 ( 2199) metal coordination : bond 0.00165 ( 3) covalent geometry : bond 0.00238 (19378) covalent geometry : angle 0.52320 (26233) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.7895 (tpt) cc_final: 0.7299 (tpt) REVERT: A 229 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7366 (tt) REVERT: A 438 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7307 (mm-30) REVERT: A 516 MET cc_start: 0.8058 (tmm) cc_final: 0.7706 (ttp) REVERT: A 727 MET cc_start: 0.7576 (mmm) cc_final: 0.7024 (mmm) REVERT: A 830 SER cc_start: 0.8987 (t) cc_final: 0.8514 (m) REVERT: A 833 ASP cc_start: 0.7527 (m-30) cc_final: 0.7088 (m-30) REVERT: A 845 LYS cc_start: 0.7824 (mptt) cc_final: 0.7573 (mmtt) REVERT: A 1032 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8139 (mt) REVERT: A 1144 MET cc_start: 0.8225 (ttm) cc_final: 0.7940 (ttp) REVERT: A 1182 ASP cc_start: 0.7019 (m-30) cc_final: 0.6173 (t0) REVERT: A 1232 TRP cc_start: 0.8518 (p-90) cc_final: 0.8225 (p-90) REVERT: A 1312 LEU cc_start: 0.7988 (mm) cc_final: 0.7765 (mt) REVERT: A 1347 ASP cc_start: 0.8470 (t0) cc_final: 0.8191 (t0) REVERT: A 1371 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.7876 (pt) REVERT: A 1655 MET cc_start: 0.7820 (tpp) cc_final: 0.7112 (ttp) REVERT: A 1666 SER cc_start: 0.9156 (m) cc_final: 0.8932 (t) REVERT: A 1917 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.7489 (m-40) REVERT: A 2069 PHE cc_start: 0.6657 (m-80) cc_final: 0.6423 (m-80) REVERT: A 2169 LYS cc_start: 0.8293 (mtpt) cc_final: 0.7885 (mtpp) REVERT: A 2184 GLN cc_start: 0.7636 (tt0) cc_final: 0.7291 (tt0) REVERT: A 2212 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.7954 (pp) REVERT: A 2271 MET cc_start: 0.8170 (ttm) cc_final: 0.7882 (ttm) REVERT: A 2282 MET cc_start: 0.7872 (mmt) cc_final: 0.7644 (mmt) REVERT: A 2302 PHE cc_start: 0.6738 (OUTLIER) cc_final: 0.5947 (t80) REVERT: A 2346 VAL cc_start: 0.2488 (OUTLIER) cc_final: 0.2248 (t) outliers start: 52 outliers final: 38 residues processed: 238 average time/residue: 0.2899 time to fit residues: 111.6023 Evaluate side-chains 235 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1517 LYS Chi-restraints excluded: chain A residue 1587 SER Chi-restraints excluded: chain A residue 1611 ILE Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1643 THR Chi-restraints excluded: chain A residue 1648 TYR Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1735 ASP Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1859 VAL Chi-restraints excluded: chain A residue 1862 ASP Chi-restraints excluded: chain A residue 1875 SER Chi-restraints excluded: chain A residue 1917 ASN Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain A residue 2212 ILE Chi-restraints excluded: chain A residue 2302 PHE Chi-restraints excluded: chain A residue 2311 LEU Chi-restraints excluded: chain A residue 2346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 98 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN A 579 HIS ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1941 ASN A2260 ASN A2268 ASN ** A2309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.106711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.091773 restraints weight = 39715.117| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.03 r_work: 0.3317 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 19381 Z= 0.176 Angle : 0.735 59.199 26233 Z= 0.437 Chirality : 0.046 0.264 2905 Planarity : 0.003 0.053 3412 Dihedral : 4.869 46.788 2556 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.59 % Favored : 94.32 % Rotamer: Outliers : 2.44 % Allowed : 14.90 % Favored : 82.66 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2361 helix: 2.11 (0.20), residues: 662 sheet: -0.30 (0.24), residues: 465 loop : -0.72 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1264 HIS 0.003 0.001 HIS A1186 PHE 0.054 0.002 PHE A1188 TYR 0.025 0.001 TYR A1957 ARG 0.007 0.000 ARG A1057 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 820) hydrogen bonds : angle 4.65433 ( 2199) metal coordination : bond 0.00243 ( 3) covalent geometry : bond 0.00390 (19378) covalent geometry : angle 0.73537 (26233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10902.31 seconds wall clock time: 192 minutes 3.28 seconds (11523.28 seconds total)