Starting phenix.real_space_refine on Sun Aug 24 10:48:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qen_18373/08_2025/8qen_18373.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qen_18373/08_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_18373/08_2025/8qen_18373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qen_18373/08_2025/8qen_18373.map" model { file = "/net/cci-nas-00/data/ceres_data/8qen_18373/08_2025/8qen_18373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qen_18373/08_2025/8qen_18373.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.015 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.16, per 1000 atoms: 0.22 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: 1.24 Conformation dependent library (CDL) restraints added in 752.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.95 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: 5.46 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 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: 8.710 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.540 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.230 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (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 ARG 0.003 0.000 ARG A1265 TYR 0.017 0.001 TYR A1648 PHE 0.017 0.002 PHE A1638 TRP 0.011 0.001 TRP A1232 HIS 0.003 0.001 HIS A2016 Details of bonding type rmsd covalent geometry : bond 0.00350 (19378) covalent geometry : angle 0.54209 (26233) hydrogen bonds : bond 0.12333 ( 820) hydrogen bonds : angle 6.77426 ( 2199) metal coordination : bond 0.22299 ( 3) *********************** 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 : 0.742 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: 0.1494 time to fit residues: 110.8670 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 : 0.678 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0270 chunk 235 optimal weight: 8.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.107942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.092857 restraints weight = 39380.735| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.04 r_work: 0.3340 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19381 Z= 0.123 Angle : 0.548 8.831 26233 Z= 0.301 Chirality : 0.045 0.150 2905 Planarity : 0.003 0.057 3412 Dihedral : 5.869 56.926 2585 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.62 % Favored : 95.26 % Rotamer: Outliers : 2.11 % Allowed : 9.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.18), residues: 2361 helix: 1.91 (0.20), residues: 654 sheet: -0.21 (0.24), residues: 454 loop : -0.31 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 751 TYR 0.027 0.002 TYR A 921 PHE 0.034 0.001 PHE A1188 TRP 0.011 0.001 TRP A1344 HIS 0.003 0.001 HIS A1126 Details of bonding type rmsd covalent geometry : bond 0.00267 (19378) covalent geometry : angle 0.54813 (26233) hydrogen bonds : bond 0.03858 ( 820) hydrogen bonds : angle 5.16596 ( 2199) metal coordination : bond 0.00377 ( 3) *********************** 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 316 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 271 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.7914 (tpt) cc_final: 0.7284 (tpt) REVERT: A 229 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7517 (tt) REVERT: A 273 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.8098 (ptp-170) REVERT: A 516 MET cc_start: 0.8155 (tmm) cc_final: 0.7892 (ttp) REVERT: A 700 MET cc_start: 0.8256 (mmm) cc_final: 0.8050 (mmt) REVERT: A 727 MET cc_start: 0.7296 (mmm) cc_final: 0.7021 (mmm) REVERT: A 751 ARG cc_start: 0.8354 (mmm-85) cc_final: 0.7697 (mmm-85) REVERT: A 830 SER cc_start: 0.8966 (t) cc_final: 0.8498 (m) REVERT: A 845 LYS cc_start: 0.8259 (mmtt) cc_final: 0.8048 (mmtt) REVERT: A 929 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8157 (mm) REVERT: A 1232 TRP cc_start: 0.8376 (p-90) cc_final: 0.8097 (p-90) REVERT: A 1332 MET cc_start: 0.8240 (ttm) cc_final: 0.7765 (ttm) REVERT: A 1347 ASP cc_start: 0.8538 (t0) cc_final: 0.8253 (t0) REVERT: A 1434 LYS cc_start: 0.8030 (mppt) cc_final: 0.7797 (mtmt) REVERT: A 1436 LEU cc_start: 0.8606 (tp) cc_final: 0.8351 (tp) REVERT: A 1655 MET cc_start: 0.7730 (tpp) cc_final: 0.7040 (ttp) REVERT: A 1925 PHE cc_start: 0.5755 (t80) cc_final: 0.5450 (t80) REVERT: A 1937 TYR cc_start: 0.6834 (t80) cc_final: 0.6589 (t80) REVERT: A 2025 MET cc_start: 0.7132 (ttp) cc_final: 0.6683 (ttt) REVERT: A 2088 TYR cc_start: 0.6404 (m-80) cc_final: 0.5981 (m-80) REVERT: A 2212 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8211 (pt) REVERT: A 2250 ILE cc_start: 0.8722 (mt) cc_final: 0.8511 (mt) REVERT: A 2271 MET cc_start: 0.8437 (ttm) cc_final: 0.8205 (ttm) REVERT: A 2280 ASP cc_start: 0.7608 (t70) cc_final: 0.7269 (t70) REVERT: A 2328 LEU cc_start: 0.7495 (mt) cc_final: 0.7223 (mt) outliers start: 45 outliers final: 19 residues processed: 302 average time/residue: 0.1164 time to fit residues: 54.8435 Evaluate side-chains 233 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 273 ARG Chi-restraints excluded: chain A residue 596 ASN 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 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 2005 MET Chi-restraints excluded: chain A residue 2147 ASN Chi-restraints excluded: chain A residue 2212 ILE Chi-restraints excluded: chain A residue 2282 MET Chi-restraints excluded: chain A residue 2320 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 203 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 215 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 214 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 385 GLN A 579 HIS A 659 ASN A1651 ASN ** A1783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1934 ASN ** A1971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3636 r_free = 0.3636 target = 0.104780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.089622 restraints weight = 39856.619| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.05 r_work: 0.3274 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 19381 Z= 0.189 Angle : 0.582 9.704 26233 Z= 0.316 Chirality : 0.047 0.183 2905 Planarity : 0.004 0.049 3412 Dihedral : 5.422 48.495 2562 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.42 % Favored : 94.45 % Rotamer: Outliers : 2.91 % Allowed : 10.31 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.17), residues: 2361 helix: 1.70 (0.20), residues: 656 sheet: -0.42 (0.24), residues: 445 loop : -0.49 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 751 TYR 0.021 0.002 TYR A2089 PHE 0.020 0.002 PHE A1638 TRP 0.012 0.001 TRP A1264 HIS 0.004 0.001 HIS A1126 Details of bonding type rmsd covalent geometry : bond 0.00443 (19378) covalent geometry : angle 0.58167 (26233) hydrogen bonds : bond 0.04225 ( 820) hydrogen bonds : angle 5.09676 ( 2199) metal coordination : bond 0.00401 ( 3) *********************** 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 275 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 213 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.7987 (tpt) cc_final: 0.7556 (tpt) REVERT: A 229 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7834 (tt) REVERT: A 448 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.6880 (mpp) REVERT: A 516 MET cc_start: 0.8150 (tmm) cc_final: 0.7846 (ttp) REVERT: A 567 SER cc_start: 0.7461 (OUTLIER) cc_final: 0.6692 (m) REVERT: A 845 LYS cc_start: 0.8370 (mmtt) cc_final: 0.8120 (mmtt) REVERT: A 929 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.8011 (mm) REVERT: A 1141 ASP cc_start: 0.6341 (t0) cc_final: 0.6032 (t0) REVERT: A 1144 MET cc_start: 0.8253 (ttp) cc_final: 0.7907 (ttp) REVERT: A 1232 TRP cc_start: 0.8429 (p-90) cc_final: 0.8168 (p-90) REVERT: A 1332 MET cc_start: 0.8351 (ttm) cc_final: 0.7874 (ttm) REVERT: A 1347 ASP cc_start: 0.8558 (t0) cc_final: 0.8304 (t0) REVERT: A 1434 LYS cc_start: 0.8070 (mppt) cc_final: 0.7789 (mtmt) REVERT: A 1462 TYR cc_start: 0.7782 (t80) cc_final: 0.7544 (t80) REVERT: A 1655 MET cc_start: 0.7787 (tpp) cc_final: 0.7136 (ttp) REVERT: A 1735 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7825 (m-30) REVERT: A 1882 ASP cc_start: 0.7138 (t0) cc_final: 0.6672 (t0) REVERT: A 2037 LYS cc_start: 0.7526 (mmtt) cc_final: 0.7317 (mmtt) REVERT: A 2271 MET cc_start: 0.8458 (ttm) cc_final: 0.8247 (ttm) outliers start: 62 outliers final: 40 residues processed: 257 average time/residue: 0.1277 time to fit residues: 51.8124 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 : 0.537 ------------------------------------------------------------------------------- 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 389 SER 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 580 TYR 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 841 ILE 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 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 1371 ILE Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1638 PHE 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 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 2059 ILE Chi-restraints excluded: chain A residue 2072 SER Chi-restraints excluded: chain A residue 2147 ASN Chi-restraints excluded: chain A residue 2192 VAL Chi-restraints excluded: chain A residue 2282 MET 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 38 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 209 optimal weight: 9.9990 chunk 230 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 A1070 ASN ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2272 GLN ** 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 = 0.3616 r_free = 0.3616 target = 0.103533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.088476 restraints weight = 40073.573| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.04 r_work: 0.3254 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19381 Z= 0.205 Angle : 0.596 10.081 26233 Z= 0.322 Chirality : 0.047 0.192 2905 Planarity : 0.004 0.051 3412 Dihedral : 5.464 51.535 2558 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.10 % Favored : 93.77 % Rotamer: Outliers : 3.23 % Allowed : 12.04 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.17), residues: 2361 helix: 1.49 (0.20), residues: 656 sheet: -0.55 (0.23), residues: 470 loop : -0.70 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1265 TYR 0.021 0.002 TYR A1648 PHE 0.043 0.002 PHE A1188 TRP 0.010 0.002 TRP A 102 HIS 0.004 0.001 HIS A1186 Details of bonding type rmsd covalent geometry : bond 0.00480 (19378) covalent geometry : angle 0.59589 (26233) hydrogen bonds : bond 0.04301 ( 820) hydrogen bonds : angle 5.14599 ( 2199) metal coordination : bond 0.00501 ( 3) *********************** 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 283 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 214 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7335 (ttt-90) REVERT: A 176 MET cc_start: 0.8006 (tpt) cc_final: 0.7535 (tpt) REVERT: A 229 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7730 (tt) REVERT: A 448 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7417 (mmm) REVERT: A 489 MET cc_start: 0.8809 (mmt) cc_final: 0.8405 (mmt) REVERT: A 516 MET cc_start: 0.8187 (tmm) cc_final: 0.7869 (ttp) REVERT: A 567 SER cc_start: 0.7725 (OUTLIER) cc_final: 0.7353 (t) REVERT: A 751 ARG cc_start: 0.8518 (mmm-85) cc_final: 0.7933 (mmm-85) REVERT: A 929 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7983 (mm) REVERT: A 1141 ASP cc_start: 0.6417 (t0) cc_final: 0.6041 (t0) REVERT: A 1144 MET cc_start: 0.8364 (ttp) cc_final: 0.8005 (ttp) REVERT: A 1182 ASP cc_start: 0.7193 (m-30) cc_final: 0.6113 (t0) REVERT: A 1232 TRP cc_start: 0.8504 (p-90) cc_final: 0.8265 (p-90) REVERT: A 1347 ASP cc_start: 0.8576 (t0) cc_final: 0.8319 (t0) REVERT: A 1434 LYS cc_start: 0.8099 (mppt) cc_final: 0.7805 (mtmt) REVERT: A 1511 ASN cc_start: 0.7810 (m110) cc_final: 0.7607 (m110) REVERT: A 1655 MET cc_start: 0.7813 (tpp) cc_final: 0.7124 (ttp) REVERT: A 2037 LYS cc_start: 0.7646 (mmtt) cc_final: 0.7323 (mmtt) REVERT: A 2169 LYS cc_start: 0.8118 (mtpt) cc_final: 0.7640 (mtpp) REVERT: A 2184 GLN cc_start: 0.7576 (tt0) cc_final: 0.7094 (tt0) REVERT: A 2271 MET cc_start: 0.8450 (ttm) cc_final: 0.8245 (ttm) REVERT: A 2280 ASP cc_start: 0.7901 (t70) cc_final: 0.7493 (t0) REVERT: A 2302 PHE cc_start: 0.6920 (OUTLIER) cc_final: 0.6121 (t80) outliers start: 69 outliers final: 47 residues processed: 259 average time/residue: 0.1160 time to fit residues: 47.8386 Evaluate side-chains 232 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 179 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 175 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 596 ASN 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 726 LEU Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 788 THR 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 1036 ILE Chi-restraints excluded: chain A residue 1063 LYS 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 1132 THR Chi-restraints excluded: chain A residue 1183 ASP Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1423 LYS Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1506 PHE Chi-restraints excluded: chain A residue 1565 ILE Chi-restraints excluded: chain A residue 1587 SER 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 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 1955 MET Chi-restraints excluded: chain A residue 2011 GLU 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 121 optimal weight: 0.0170 chunk 144 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 171 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1651 ASN A1971 GLN A2272 GLN A2292 GLN ** A2314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.105865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.090914 restraints weight = 39548.978| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.01 r_work: 0.3303 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19381 Z= 0.116 Angle : 0.525 11.006 26233 Z= 0.285 Chirality : 0.045 0.160 2905 Planarity : 0.003 0.050 3412 Dihedral : 5.148 52.180 2556 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.34 % Favored : 94.54 % Rotamer: Outliers : 2.72 % Allowed : 13.54 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.17), residues: 2361 helix: 1.80 (0.20), residues: 660 sheet: -0.52 (0.23), residues: 460 loop : -0.66 (0.18), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1057 TYR 0.024 0.001 TYR A2089 PHE 0.043 0.001 PHE A1188 TRP 0.009 0.001 TRP A 102 HIS 0.004 0.001 HIS A1126 Details of bonding type rmsd covalent geometry : bond 0.00254 (19378) covalent geometry : angle 0.52528 (26233) hydrogen bonds : bond 0.03554 ( 820) hydrogen bonds : angle 4.89572 ( 2199) metal coordination : bond 0.00125 ( 3) *********************** 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 271 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 213 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.7925 (tpt) cc_final: 0.7309 (tpt) REVERT: A 229 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7509 (tt) REVERT: A 448 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7193 (mmm) REVERT: A 489 MET cc_start: 0.8815 (mmt) cc_final: 0.8413 (mmt) REVERT: A 516 MET cc_start: 0.8140 (tmm) cc_final: 0.7778 (ttp) REVERT: A 727 MET cc_start: 0.7484 (mmm) cc_final: 0.6876 (mmm) REVERT: A 830 SER cc_start: 0.8969 (t) cc_final: 0.8543 (m) REVERT: A 929 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7737 (mm) REVERT: A 1099 ILE cc_start: 0.7237 (OUTLIER) cc_final: 0.6554 (mm) REVERT: A 1141 ASP cc_start: 0.6059 (t0) cc_final: 0.5261 (t0) REVERT: A 1144 MET cc_start: 0.8255 (ttp) cc_final: 0.7891 (ttp) REVERT: A 1182 ASP cc_start: 0.7083 (m-30) cc_final: 0.6089 (t0) REVERT: A 1232 TRP cc_start: 0.8464 (p-90) cc_final: 0.8207 (p-90) REVERT: A 1347 ASP cc_start: 0.8495 (t0) cc_final: 0.8224 (t0) REVERT: A 1434 LYS cc_start: 0.7996 (mppt) cc_final: 0.7750 (mtmt) REVERT: A 1511 ASN cc_start: 0.7714 (m110) cc_final: 0.7497 (m110) REVERT: A 1588 MET cc_start: 0.7554 (mmp) cc_final: 0.7198 (mmp) REVERT: A 1655 MET cc_start: 0.7829 (tpp) cc_final: 0.7134 (ttp) REVERT: A 1739 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8187 (ptm-80) REVERT: A 2037 LYS cc_start: 0.7573 (mmtt) cc_final: 0.7314 (mmtt) REVERT: A 2169 LYS cc_start: 0.8115 (mtpt) cc_final: 0.7670 (mtpp) REVERT: A 2184 GLN cc_start: 0.7491 (tt0) cc_final: 0.7091 (tt0) REVERT: A 2271 MET cc_start: 0.8308 (ttm) cc_final: 0.8095 (ttm) REVERT: A 2302 PHE cc_start: 0.6880 (OUTLIER) cc_final: 0.5776 (t80) outliers start: 58 outliers final: 36 residues processed: 251 average time/residue: 0.1127 time to fit residues: 44.9593 Evaluate side-chains 230 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 389 SER Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 596 ASN 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 841 ILE 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 1073 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1145 MET Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1587 SER 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 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 2011 GLU 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 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 217 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 118 optimal weight: 0.3980 chunk 93 optimal weight: 4.9990 chunk 183 optimal weight: 0.2980 chunk 153 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1651 ASN ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 ASN ** 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 = 0.3644 r_free = 0.3644 target = 0.105222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.090208 restraints weight = 39636.628| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.03 r_work: 0.3287 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: 0.7811 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19381 Z= 0.134 Angle : 0.531 10.413 26233 Z= 0.288 Chirality : 0.045 0.166 2905 Planarity : 0.003 0.049 3412 Dihedral : 5.133 51.680 2556 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.76 % Favored : 94.11 % Rotamer: Outliers : 3.05 % Allowed : 13.96 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.18), residues: 2361 helix: 1.73 (0.20), residues: 670 sheet: -0.50 (0.24), residues: 458 loop : -0.70 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 751 TYR 0.021 0.001 TYR A 742 PHE 0.044 0.001 PHE A1188 TRP 0.008 0.001 TRP A 102 HIS 0.004 0.001 HIS A1126 Details of bonding type rmsd covalent geometry : bond 0.00308 (19378) covalent geometry : angle 0.53104 (26233) hydrogen bonds : bond 0.03660 ( 820) hydrogen bonds : angle 4.82871 ( 2199) metal coordination : bond 0.00255 ( 3) *********************** 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 269 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 204 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7301 (ttt-90) REVERT: A 176 MET cc_start: 0.7927 (tpt) cc_final: 0.7454 (tpt) REVERT: A 229 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7573 (tt) REVERT: A 329 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.5903 (pp20) REVERT: A 489 MET cc_start: 0.8824 (mmt) cc_final: 0.8337 (mmt) REVERT: A 516 MET cc_start: 0.8165 (tmm) cc_final: 0.7823 (ttp) REVERT: A 567 SER cc_start: 0.7659 (OUTLIER) cc_final: 0.7322 (t) REVERT: A 727 MET cc_start: 0.7562 (mmm) cc_final: 0.6996 (mmm) REVERT: A 751 ARG cc_start: 0.8449 (mmm-85) cc_final: 0.7956 (mmm-85) REVERT: A 830 SER cc_start: 0.9030 (t) cc_final: 0.8556 (m) REVERT: A 845 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7987 (mmtt) REVERT: A 929 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7675 (mm) REVERT: A 1141 ASP cc_start: 0.6174 (t0) cc_final: 0.5422 (t0) REVERT: A 1144 MET cc_start: 0.8251 (ttp) cc_final: 0.7875 (ttp) REVERT: A 1182 ASP cc_start: 0.7141 (m-30) cc_final: 0.6147 (t0) REVERT: A 1232 TRP cc_start: 0.8556 (p-90) cc_final: 0.8348 (p-90) REVERT: A 1347 ASP cc_start: 0.8508 (t0) cc_final: 0.8233 (t0) REVERT: A 1434 LYS cc_start: 0.8032 (mppt) cc_final: 0.7758 (mtmt) REVERT: A 1655 MET cc_start: 0.7862 (tpp) cc_final: 0.7150 (ttp) REVERT: A 1666 SER cc_start: 0.9134 (m) cc_final: 0.8883 (t) REVERT: A 1739 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8198 (ptm-80) REVERT: A 2037 LYS cc_start: 0.7594 (mmtt) cc_final: 0.7247 (mmtt) REVERT: A 2069 PHE cc_start: 0.6245 (m-80) cc_final: 0.5932 (m-80) REVERT: A 2169 LYS cc_start: 0.8170 (mtpt) cc_final: 0.7714 (mtpp) REVERT: A 2184 GLN cc_start: 0.7574 (tt0) cc_final: 0.7100 (tt0) REVERT: A 2271 MET cc_start: 0.8280 (ttm) cc_final: 0.8048 (ttm) REVERT: A 2302 PHE cc_start: 0.6787 (OUTLIER) cc_final: 0.5829 (t80) REVERT: A 2346 VAL cc_start: 0.2251 (OUTLIER) cc_final: 0.2037 (t) outliers start: 65 outliers final: 46 residues processed: 248 average time/residue: 0.1141 time to fit residues: 44.9957 Evaluate side-chains 239 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 185 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 175 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain A residue 929 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 1073 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1145 MET 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 1587 SER 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 1739 ARG 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 2005 MET Chi-restraints excluded: chain A residue 2011 GLU Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain A residue 2072 SER Chi-restraints excluded: chain A residue 2116 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 187 optimal weight: 10.0000 chunk 143 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1997 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2260 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.105764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.090761 restraints weight = 39900.276| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.05 r_work: 0.3298 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19381 Z= 0.123 Angle : 0.522 10.453 26233 Z= 0.283 Chirality : 0.045 0.162 2905 Planarity : 0.003 0.048 3412 Dihedral : 5.031 50.634 2556 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.89 % Favored : 94.03 % Rotamer: Outliers : 2.91 % Allowed : 14.48 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.18), residues: 2361 helix: 1.88 (0.20), residues: 663 sheet: -0.42 (0.24), residues: 453 loop : -0.71 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 751 TYR 0.022 0.001 TYR A 742 PHE 0.045 0.001 PHE A1188 TRP 0.007 0.001 TRP A2325 HIS 0.004 0.001 HIS A1126 Details of bonding type rmsd covalent geometry : bond 0.00277 (19378) covalent geometry : angle 0.52159 (26233) hydrogen bonds : bond 0.03490 ( 820) hydrogen bonds : angle 4.75974 ( 2199) metal coordination : bond 0.00197 ( 3) *********************** 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 267 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 205 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.7900 (tpt) cc_final: 0.7478 (tpt) REVERT: A 229 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7466 (tt) REVERT: A 329 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.6063 (pp20) REVERT: A 516 MET cc_start: 0.8134 (tmm) cc_final: 0.7797 (ttp) REVERT: A 581 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7702 (mt) REVERT: A 727 MET cc_start: 0.7571 (mmm) cc_final: 0.7033 (mmm) REVERT: A 751 ARG cc_start: 0.8289 (mmm-85) cc_final: 0.7772 (mmm-85) REVERT: A 830 SER cc_start: 0.9011 (t) cc_final: 0.8550 (m) REVERT: A 845 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7962 (mmtt) REVERT: A 1144 MET cc_start: 0.8227 (ttp) cc_final: 0.7830 (ttp) REVERT: A 1182 ASP cc_start: 0.7126 (m-30) cc_final: 0.6181 (t0) REVERT: A 1347 ASP cc_start: 0.8485 (t0) cc_final: 0.8206 (t0) REVERT: A 1371 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.7776 (pt) REVERT: A 1434 LYS cc_start: 0.8051 (mppt) cc_final: 0.7794 (mtmt) REVERT: A 1588 MET cc_start: 0.7616 (mmp) cc_final: 0.7260 (mmp) REVERT: A 1655 MET cc_start: 0.7902 (tpp) cc_final: 0.7395 (ttm) REVERT: A 1666 SER cc_start: 0.9120 (m) cc_final: 0.8867 (t) REVERT: A 1739 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8207 (ptm-80) REVERT: A 1931 ILE cc_start: 0.8499 (mt) cc_final: 0.8283 (mt) REVERT: A 2037 LYS cc_start: 0.7538 (mmtt) cc_final: 0.7215 (mmtt) REVERT: A 2069 PHE cc_start: 0.6353 (m-80) cc_final: 0.6071 (m-80) REVERT: A 2169 LYS cc_start: 0.8243 (mtpt) cc_final: 0.7826 (mtpp) REVERT: A 2184 GLN cc_start: 0.7495 (tt0) cc_final: 0.7157 (tt0) REVERT: A 2271 MET cc_start: 0.8204 (ttm) cc_final: 0.7950 (ttm) REVERT: A 2282 MET cc_start: 0.7965 (mmt) cc_final: 0.7106 (mmt) REVERT: A 2302 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.5761 (t80) REVERT: A 2329 ASP cc_start: 0.7616 (m-30) cc_final: 0.7030 (t0) REVERT: A 2346 VAL cc_start: 0.2616 (OUTLIER) cc_final: 0.1795 (p) outliers start: 62 outliers final: 41 residues processed: 248 average time/residue: 0.1139 time to fit residues: 45.0624 Evaluate side-chains 238 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 190 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 329 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 636 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 724 SER Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 952 THR 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 1129 LEU Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1145 MET 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 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 1739 ARG 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 2005 MET Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain A residue 2072 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 133 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN A 579 HIS A 596 ASN ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1651 ASN ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1941 ASN ** A1997 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2260 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.101238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.086294 restraints weight = 40335.343| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.02 r_work: 0.3212 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 19381 Z= 0.293 Angle : 0.678 11.965 26233 Z= 0.366 Chirality : 0.050 0.246 2905 Planarity : 0.004 0.054 3412 Dihedral : 5.748 52.393 2556 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.45 % Favored : 92.46 % Rotamer: Outliers : 3.61 % Allowed : 13.78 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.17), residues: 2361 helix: 1.07 (0.19), residues: 667 sheet: -0.72 (0.23), residues: 478 loop : -0.97 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1265 TYR 0.036 0.002 TYR A 742 PHE 0.048 0.003 PHE A1188 TRP 0.022 0.002 TRP A1232 HIS 0.009 0.002 HIS A1556 Details of bonding type rmsd covalent geometry : bond 0.00694 (19378) covalent geometry : angle 0.67806 (26233) hydrogen bonds : bond 0.04914 ( 820) hydrogen bonds : angle 5.38725 ( 2199) metal coordination : bond 0.00716 ( 3) *********************** 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 268 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 191 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: A 176 MET cc_start: 0.8028 (tpt) cc_final: 0.7617 (tpt) REVERT: A 229 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7724 (tt) REVERT: A 329 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6237 (pp20) REVERT: A 338 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8331 (mt) REVERT: A 516 MET cc_start: 0.8177 (tmm) cc_final: 0.7862 (ttp) REVERT: A 845 LYS cc_start: 0.8445 (mmtt) cc_final: 0.8130 (mmtt) REVERT: A 929 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8227 (mm) REVERT: A 1141 ASP cc_start: 0.6338 (t0) cc_final: 0.5601 (t0) REVERT: A 1144 MET cc_start: 0.8383 (ttp) cc_final: 0.8096 (ttp) REVERT: A 1182 ASP cc_start: 0.7182 (m-30) cc_final: 0.6213 (t0) REVERT: A 1347 ASP cc_start: 0.8568 (t0) cc_final: 0.8327 (t0) REVERT: A 1434 LYS cc_start: 0.8185 (mppt) cc_final: 0.7925 (mtmt) REVERT: A 1655 MET cc_start: 0.7621 (tpp) cc_final: 0.7088 (ttp) REVERT: A 1666 SER cc_start: 0.9133 (m) cc_final: 0.8901 (t) REVERT: A 1824 TYR cc_start: 0.7329 (m-80) cc_final: 0.6683 (m-80) REVERT: A 2162 PHE cc_start: 0.6797 (m-80) cc_final: 0.6565 (m-80) REVERT: A 2169 LYS cc_start: 0.8282 (mtpt) cc_final: 0.7937 (mttm) REVERT: A 2184 GLN cc_start: 0.7634 (tt0) cc_final: 0.7120 (tt0) REVERT: A 2212 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8041 (pp) REVERT: A 2271 MET cc_start: 0.8504 (ttm) cc_final: 0.8045 (ttm) REVERT: A 2282 MET cc_start: 0.7974 (mmt) cc_final: 0.7124 (mmt) REVERT: A 2302 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6271 (t80) REVERT: A 2329 ASP cc_start: 0.7672 (m-30) cc_final: 0.6921 (t70) outliers start: 77 outliers final: 54 residues processed: 247 average time/residue: 0.1184 time to fit residues: 47.1289 Evaluate side-chains 241 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 180 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 243 PHE Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 636 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 724 SER 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 929 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 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 1145 MET Chi-restraints excluded: chain A residue 1183 ASP Chi-restraints excluded: chain A residue 1248 THR 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 1471 GLU Chi-restraints excluded: chain A residue 1506 PHE Chi-restraints excluded: chain A residue 1517 LYS Chi-restraints excluded: chain A residue 1587 SER 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 1739 ARG 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 1876 ILE Chi-restraints excluded: chain A residue 2005 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 204 optimal weight: 4.9990 chunk 168 optimal weight: 0.7980 chunk 184 optimal weight: 0.4980 chunk 172 optimal weight: 1.9990 chunk 180 optimal weight: 0.1980 chunk 101 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1941 ASN ** A1997 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2260 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.105486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.090530 restraints weight = 39630.530| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.02 r_work: 0.3294 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19381 Z= 0.118 Angle : 0.533 11.560 26233 Z= 0.289 Chirality : 0.045 0.156 2905 Planarity : 0.003 0.048 3412 Dihedral : 5.172 53.426 2556 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.46 % Favored : 94.45 % Rotamer: Outliers : 2.62 % Allowed : 14.85 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.17), residues: 2361 helix: 1.65 (0.20), residues: 662 sheet: -0.63 (0.24), residues: 456 loop : -0.80 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 751 TYR 0.023 0.001 TYR A 742 PHE 0.046 0.001 PHE A1188 TRP 0.031 0.002 TRP A1232 HIS 0.003 0.001 HIS A1126 Details of bonding type rmsd covalent geometry : bond 0.00262 (19378) covalent geometry : angle 0.53281 (26233) hydrogen bonds : bond 0.03513 ( 820) hydrogen bonds : angle 4.89864 ( 2199) metal coordination : bond 0.00183 ( 3) *********************** 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 262 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 SER cc_start: 0.8712 (t) cc_final: 0.8428 (p) REVERT: A 176 MET cc_start: 0.7868 (tpt) cc_final: 0.7301 (tpt) REVERT: A 229 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7556 (tt) REVERT: A 329 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.6045 (pp20) REVERT: A 338 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8199 (mt) REVERT: A 438 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7335 (mm-30) REVERT: A 489 MET cc_start: 0.8806 (mmt) cc_final: 0.8144 (mmp) REVERT: A 516 MET cc_start: 0.8114 (tmm) cc_final: 0.7762 (tpp) REVERT: A 727 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7195 (mmm) REVERT: A 830 SER cc_start: 0.9000 (t) cc_final: 0.8556 (m) REVERT: A 845 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7908 (mmtt) REVERT: A 1144 MET cc_start: 0.8298 (ttp) cc_final: 0.7919 (ttp) REVERT: A 1182 ASP cc_start: 0.7095 (m-30) cc_final: 0.6187 (t0) REVERT: A 1307 TYR cc_start: 0.7574 (t80) cc_final: 0.7306 (t80) REVERT: A 1347 ASP cc_start: 0.8500 (t0) cc_final: 0.8222 (t0) REVERT: A 1371 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.7942 (pt) REVERT: A 1434 LYS cc_start: 0.8011 (mppt) cc_final: 0.7745 (mtmt) REVERT: A 1588 MET cc_start: 0.7567 (mmp) cc_final: 0.7181 (mmp) REVERT: A 1666 SER cc_start: 0.9027 (m) cc_final: 0.8807 (t) REVERT: A 2037 LYS cc_start: 0.7600 (mmtt) cc_final: 0.7311 (mmtt) REVERT: A 2162 PHE cc_start: 0.6829 (m-80) cc_final: 0.6626 (m-80) REVERT: A 2169 LYS cc_start: 0.8291 (mtpt) cc_final: 0.7891 (mtpp) REVERT: A 2184 GLN cc_start: 0.7322 (tt0) cc_final: 0.7065 (tt0) REVERT: A 2271 MET cc_start: 0.8259 (ttm) cc_final: 0.8002 (ttm) REVERT: A 2282 MET cc_start: 0.7891 (mmt) cc_final: 0.7089 (mmt) REVERT: A 2302 PHE cc_start: 0.6868 (OUTLIER) cc_final: 0.5850 (t80) REVERT: A 2328 LEU cc_start: 0.7499 (mt) cc_final: 0.7291 (mt) REVERT: A 2329 ASP cc_start: 0.7590 (m-30) cc_final: 0.6821 (t70) REVERT: A 2346 VAL cc_start: 0.2592 (OUTLIER) cc_final: 0.2368 (t) outliers start: 56 outliers final: 41 residues processed: 244 average time/residue: 0.1098 time to fit residues: 42.5427 Evaluate side-chains 240 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 243 PHE Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 596 ASN 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 724 SER Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 952 THR 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 1145 MET 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 1471 GLU Chi-restraints excluded: chain A residue 1517 LYS Chi-restraints excluded: chain A residue 1587 SER 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 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 2005 MET Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain A residue 2072 SER Chi-restraints excluded: chain A residue 2192 VAL Chi-restraints excluded: chain A residue 2260 ASN Chi-restraints excluded: chain A residue 2302 PHE 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 15 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 chunk 190 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN A1523 ASN ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1651 ASN ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1941 ASN ** A1997 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2260 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.105176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.090199 restraints weight = 39794.219| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.03 r_work: 0.3288 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19381 Z= 0.130 Angle : 0.540 11.402 26233 Z= 0.293 Chirality : 0.045 0.163 2905 Planarity : 0.003 0.051 3412 Dihedral : 5.125 52.902 2556 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.10 % Favored : 93.82 % Rotamer: Outliers : 2.53 % Allowed : 15.14 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.17), residues: 2361 helix: 1.70 (0.20), residues: 669 sheet: -0.56 (0.24), residues: 456 loop : -0.83 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1057 TYR 0.028 0.001 TYR A2170 PHE 0.048 0.001 PHE A1188 TRP 0.037 0.002 TRP A1232 HIS 0.003 0.001 HIS A1556 Details of bonding type rmsd covalent geometry : bond 0.00298 (19378) covalent geometry : angle 0.54049 (26233) hydrogen bonds : bond 0.03595 ( 820) hydrogen bonds : angle 4.87584 ( 2199) metal coordination : bond 0.00233 ( 3) ********************** 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 251 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 SER cc_start: 0.8612 (t) cc_final: 0.8358 (p) REVERT: A 176 MET cc_start: 0.7890 (tpt) cc_final: 0.7306 (tpt) REVERT: A 229 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7566 (tt) REVERT: A 329 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.6067 (pp20) REVERT: A 338 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8152 (mt) REVERT: A 438 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7349 (mm-30) REVERT: A 516 MET cc_start: 0.8160 (tmm) cc_final: 0.7811 (ttp) REVERT: A 727 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7153 (mmm) REVERT: A 830 SER cc_start: 0.8993 (t) cc_final: 0.8560 (m) REVERT: A 845 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7943 (mmtt) REVERT: A 1144 MET cc_start: 0.8267 (ttp) cc_final: 0.7889 (ttp) REVERT: A 1182 ASP cc_start: 0.7132 (m-30) cc_final: 0.6210 (t0) REVERT: A 1307 TYR cc_start: 0.7676 (t80) cc_final: 0.7293 (t80) REVERT: A 1347 ASP cc_start: 0.8512 (t0) cc_final: 0.8234 (t0) REVERT: A 1371 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.7875 (pt) REVERT: A 1434 LYS cc_start: 0.8058 (mppt) cc_final: 0.7740 (mtmt) REVERT: A 1462 TYR cc_start: 0.7825 (t80) cc_final: 0.7574 (t80) REVERT: A 1523 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8204 (m110) REVERT: A 1655 MET cc_start: 0.7996 (ttm) cc_final: 0.7619 (ttp) REVERT: A 1666 SER cc_start: 0.9035 (m) cc_final: 0.8828 (t) REVERT: A 1925 PHE cc_start: 0.5892 (t80) cc_final: 0.5537 (t80) REVERT: A 2037 LYS cc_start: 0.7564 (mmtt) cc_final: 0.7216 (mmtt) REVERT: A 2049 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7173 (tm-30) REVERT: A 2162 PHE cc_start: 0.7031 (m-80) cc_final: 0.6795 (m-80) REVERT: A 2169 LYS cc_start: 0.8312 (mtpt) cc_final: 0.7898 (mtpp) REVERT: A 2184 GLN cc_start: 0.7384 (tt0) cc_final: 0.7093 (tt0) REVERT: A 2271 MET cc_start: 0.8207 (ttm) cc_final: 0.7951 (ttm) REVERT: A 2282 MET cc_start: 0.7893 (mmt) cc_final: 0.7044 (mmt) REVERT: A 2302 PHE cc_start: 0.6964 (OUTLIER) cc_final: 0.5941 (t80) REVERT: A 2329 ASP cc_start: 0.7482 (m-30) cc_final: 0.6584 (t0) REVERT: A 2346 VAL cc_start: 0.2562 (OUTLIER) cc_final: 0.2340 (t) outliers start: 54 outliers final: 41 residues processed: 235 average time/residue: 0.1162 time to fit residues: 43.9772 Evaluate side-chains 237 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 243 PHE Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 596 ASN 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 724 SER Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 952 THR 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 1129 LEU Chi-restraints excluded: chain A residue 1145 MET 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 1471 GLU Chi-restraints excluded: chain A residue 1517 LYS Chi-restraints excluded: chain A residue 1523 ASN Chi-restraints excluded: chain A residue 1587 SER 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 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 2005 MET Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain A residue 2072 SER Chi-restraints excluded: chain A residue 2192 VAL Chi-restraints excluded: chain A residue 2260 ASN Chi-restraints excluded: chain A residue 2302 PHE 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 164 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 205 optimal weight: 0.3980 chunk 61 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1523 ASN ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2260 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.105716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.090789 restraints weight = 39735.702| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.03 r_work: 0.3296 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19381 Z= 0.119 Angle : 0.536 11.465 26233 Z= 0.289 Chirality : 0.045 0.161 2905 Planarity : 0.003 0.050 3412 Dihedral : 5.051 52.306 2556 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.51 % Favored : 94.41 % Rotamer: Outliers : 2.53 % Allowed : 15.32 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.18), residues: 2361 helix: 1.82 (0.20), residues: 664 sheet: -0.52 (0.24), residues: 456 loop : -0.80 (0.18), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1057 TYR 0.026 0.001 TYR A 742 PHE 0.030 0.001 PHE A1188 TRP 0.045 0.002 TRP A1232 HIS 0.003 0.001 HIS A1126 Details of bonding type rmsd covalent geometry : bond 0.00268 (19378) covalent geometry : angle 0.53611 (26233) hydrogen bonds : bond 0.03494 ( 820) hydrogen bonds : angle 4.81146 ( 2199) metal coordination : bond 0.00186 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4081.57 seconds wall clock time: 71 minutes 6.61 seconds (4266.61 seconds total)