Starting phenix.real_space_refine on Sun Aug 24 11:07:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jb5_36141/08_2025/8jb5_36141.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jb5_36141/08_2025/8jb5_36141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jb5_36141/08_2025/8jb5_36141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jb5_36141/08_2025/8jb5_36141.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jb5_36141/08_2025/8jb5_36141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jb5_36141/08_2025/8jb5_36141.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 47 5.16 5 C 12183 2.51 5 N 3022 2.21 5 O 3774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 324 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: 19027 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 19026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2355, 19026 Classifications: {'peptide': 2355} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 2298} Chain breaks: 1 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 5704 SG CYS A 698 81.942 22.758 87.073 1.00 23.67 S Time building chain proxies: 4.19, per 1000 atoms: 0.22 Number of scatterers: 19027 At special positions: 0 Unit cell: (180.442, 161.963, 208.704, 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 47 16.00 O 3774 8.00 N 3022 7.00 C 12183 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 988.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3000 " pdb="ZN ZN A3000 " - pdb=" SG CYS A 698 " pdb="ZN ZN A3000 " - pdb=" NE2 HIS A 757 " pdb="ZN ZN A3000 " - pdb=" ND1 HIS A 653 " 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4446 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 44 sheets defined 31.8% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 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 87 Processing helix chain 'A' and resid 108 through 122 removed outlier: 3.902A pdb=" N GLN A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TRP A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 156 removed outlier: 3.553A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 197 Processing helix chain 'A' and resid 201 through 214 removed outlier: 3.521A pdb=" N ILE A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 264 through 280 removed outlier: 3.976A pdb=" N ILE A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 324 Processing helix chain 'A' and resid 339 through 353 removed outlier: 3.967A pdb=" N SER A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 393 through 420 removed outlier: 3.533A pdb=" N ASP A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Proline residue: A 416 - end of helix Processing helix chain 'A' and resid 423 through 438 Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 470 through 484 removed outlier: 3.955A pdb=" N TYR A 474 " --> pdb=" O GLY A 470 " (cutoff:3.500A) 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 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 512 through 519 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 558 through 568 Processing helix chain 'A' and resid 587 through 601 removed outlier: 3.833A pdb=" N ASP A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 642 removed outlier: 4.531A pdb=" N ASN A 642 " --> pdb=" O TYR A 638 " (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: 4.662A pdb=" N ASP A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ARG 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 775 removed outlier: 3.778A pdb=" N LYS A 775 " --> pdb=" O ASP A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 809 removed outlier: 3.511A pdb=" N LEU A 797 " --> pdb=" O TYR A 793 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 839 Processing helix chain 'A' and resid 850 through 876 removed outlier: 3.704A pdb=" N ASN A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 936 removed outlier: 3.542A pdb=" N ALA A 922 " --> pdb=" O PHE A 918 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 926 " --> pdb=" O ALA A 922 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A 935 " --> pdb=" O ASN A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 971 removed outlier: 4.418A pdb=" N THR A 958 " --> pdb=" O HIS A 954 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 965 " --> pdb=" O SER A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 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 1042 through 1051 removed outlier: 3.513A pdb=" N GLU A1050 " --> pdb=" O LYS A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1065 Processing helix chain 'A' and resid 1072 through 1087 Processing helix chain 'A' and resid 1116 through 1133 removed outlier: 4.213A pdb=" N ALA A1130 " --> pdb=" O HIS A1126 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLU A1131 " --> pdb=" O ILE A1127 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR A1132 " --> pdb=" O SER A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 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 1348 through 1352 Processing helix chain 'A' and resid 1370 through 1373 Processing helix chain 'A' and resid 1432 through 1439 Processing helix chain 'A' and resid 1439 through 1450 removed outlier: 3.748A pdb=" N ILE A1450 " --> pdb=" O LYS A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1558 through 1572 Processing helix chain 'A' and resid 1580 through 1589 Processing helix chain 'A' and resid 1651 through 1653 No H-bonds generated for 'chain 'A' and resid 1651 through 1653' Processing helix chain 'A' and resid 1680 through 1683 Processing helix chain 'A' and resid 1685 through 1689 removed outlier: 3.758A pdb=" N VAL A1689 " --> pdb=" O ASP A1686 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1779 removed outlier: 3.871A pdb=" N ALA A1778 " --> pdb=" O SER A1774 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A1779 " --> pdb=" O ASP A1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1774 through 1779' Processing helix chain 'A' and resid 1792 through 1800 Processing helix chain 'A' and resid 1868 through 1872 removed outlier: 3.588A pdb=" N SER A1872 " --> pdb=" O PRO A1869 " (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: 6.170A pdb=" N LEU A 98 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N PHE A 130 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE A 100 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ILE A 101 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N GLN A 385 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 11.302A pdb=" N LYS A 374 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 360 through 361 removed outlier: 4.520A pdb=" N GLY A 292 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 290 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 605 through 609 removed outlier: 6.746A pdb=" N ILE A 646 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ASN A 694 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU A 648 " --> pdb=" O ASN A 694 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LEU A 696 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 650 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 617 through 622 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: 4.610A 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 938 through 940 removed outlier: 3.810A pdb=" N ASP A 938 " --> pdb=" O VAL A 945 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1035 through 1036 Processing sheet with id=AB3, first strand: chain 'A' and resid 1067 through 1068 removed outlier: 5.485A pdb=" N ASP A1515 " --> pdb=" O ASN A1530 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN A1530 " --> pdb=" O ASP A1515 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LYS A1525 " --> pdb=" O ILE A1544 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE A1544 " --> pdb=" O LYS A1525 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LYS A1537 " --> pdb=" O LEU A1557 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU A1557 " --> pdb=" O LYS A1537 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N SER A1539 " --> pdb=" O VAL A1555 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL A1555 " --> pdb=" O SER A1539 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER A1541 " --> pdb=" O ASN A1553 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N GLY A1554 " --> pdb=" O ASP A1608 " (cutoff:3.500A) removed outlier: 11.142A pdb=" N ASN A1610 " --> pdb=" O GLY A1554 " (cutoff:3.500A) removed outlier: 11.055A pdb=" N TYR A1556 " --> pdb=" O ASN A1610 " (cutoff:3.500A) removed outlier: 11.380A pdb=" N ILE A1612 " --> pdb=" O TYR A1556 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE A1611 " --> pdb=" O CYS A1626 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N CYS A1626 " --> pdb=" O PHE A1611 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLN A1621 " --> pdb=" O ILE A1637 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE A1637 " --> pdb=" O GLN A1621 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU A1623 " --> pdb=" O TYR A1635 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A1656 " --> pdb=" O ILE A1693 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A1718 " --> pdb=" O ARG A1767 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N SER A1801 " --> pdb=" O TYR A1741 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1105 through 1107 Processing sheet with id=AB5, first strand: chain 'A' and resid 1136 through 1139 removed outlier: 6.963A pdb=" N ILE A1144 " --> pdb=" O VAL A1221 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A1345 " --> pdb=" O TYR A1323 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A1325 " --> pdb=" O VAL A1345 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP A1347 " --> pdb=" O LEU A1325 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP A1344 " --> pdb=" O SER A1403 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N THR A1405 " --> pdb=" O TRP A1344 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE A1346 " --> pdb=" O THR A1405 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N SER A1407 " --> pdb=" O ILE A1346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1161 through 1164 removed outlier: 6.950A pdb=" N SER A1161 " --> pdb=" O ILE A1155 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE A1155 " --> pdb=" O SER A1161 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR A1163 " --> pdb=" O SER A1153 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER A1153 " --> pdb=" O ARG A1288 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASN A1290 " --> pdb=" O SER A1153 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE A1155 " --> pdb=" O ASN A1290 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR A1314 " --> pdb=" O ASP A1335 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ASN A1337 " --> pdb=" O TYR A1314 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N PHE A1316 " --> pdb=" O ASN A1337 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR A1388 " --> pdb=" O ILE A1334 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N LEU A1336 " --> pdb=" O THR A1388 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASN A1390 " --> pdb=" O LEU A1336 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU A1338 " --> pdb=" O ASN A1390 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR A1392 " --> pdb=" O LEU A1338 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1168 through 1169 Processing sheet with id=AB8, first strand: chain 'A' and resid 1171 through 1173 Processing sheet with id=AB9, first strand: chain 'A' and resid 1179 through 1181 removed outlier: 6.650A pdb=" N ASP A1185 " --> pdb=" O PHE A1267 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ILE A1275 " --> pdb=" O GLY A1235 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLY A1235 " --> pdb=" O ILE A1275 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1353 through 1358 removed outlier: 4.242A pdb=" N ASN A1354 " --> pdb=" O GLY A1365 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1459 through 1466 Processing sheet with id=AC3, first strand: chain 'A' and resid 1674 through 1678 removed outlier: 6.400A pdb=" N ILE A1675 " --> pdb=" O ASN A1704 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N THR A1706 " --> pdb=" O ILE A1675 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE A1677 " --> pdb=" O THR A1706 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A1703 " --> pdb=" O ASN A1733 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE A1730 " --> pdb=" O SER A1782 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASN A1784 " --> pdb=" O ILE A1730 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL A1732 " --> pdb=" O ASN A1784 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 1815 through 1819 Processing sheet with id=AC5, first strand: chain 'A' and resid 1835 through 1839 removed outlier: 3.722A pdb=" N ASN A1852 " --> pdb=" O LYS A1847 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1856 through 1860 Processing sheet with id=AC7, first strand: chain 'A' and resid 1878 through 1882 Processing sheet with id=AC8, first strand: chain 'A' and resid 1898 through 1902 removed outlier: 3.765A pdb=" N GLU A1922 " --> pdb=" O ALA A1910 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1928 through 1932 Processing sheet with id=AD1, first strand: chain 'A' and resid 1969 through 1973 removed outlier: 4.567A pdb=" N TYR A1979 " --> pdb=" O GLN A1987 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1991 through 1992 Processing sheet with id=AD3, first strand: chain 'A' and resid 2009 through 2013 Processing sheet with id=AD4, first strand: chain 'A' and resid 2029 through 2033 Processing sheet with id=AD5, first strand: chain 'A' and resid 2059 through 2063 Processing sheet with id=AD6, first strand: chain 'A' and resid 2079 through 2082 Processing sheet with id=AD7, first strand: chain 'A' and resid 2101 through 2105 Processing sheet with id=AD8, first strand: chain 'A' and resid 2143 through 2145 Processing sheet with id=AD9, first strand: chain 'A' and resid 2161 through 2165 removed outlier: 4.695A pdb=" N TYR A2171 " --> pdb=" O VAL A2187 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A2185 " --> pdb=" O ALA A2173 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 2191 through 2194 Processing sheet with id=AE2, first strand: chain 'A' and resid 2211 through 2215 Processing sheet with id=AE3, first strand: chain 'A' and resid 2232 through 2236 Processing sheet with id=AE4, first strand: chain 'A' and resid 2252 through 2256 Processing sheet with id=AE5, first strand: chain 'A' and resid 2272 through 2276 Processing sheet with id=AE6, first strand: chain 'A' and resid 2292 through 2296 removed outlier: 4.544A pdb=" N TYR A2302 " --> pdb=" O ILE A2318 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 2322 through 2326 Processing sheet with id=AE8, first strand: chain 'A' and resid 2343 through 2346 832 hydrogen bonds defined for protein. 2232 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: 7.59 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4718 1.33 - 1.45: 3944 1.45 - 1.57: 10663 1.57 - 1.69: 0 1.69 - 1.82: 84 Bond restraints: 19409 Sorted by residual: bond pdb=" C ILE A 409 " pdb=" O ILE A 409 " ideal model delta sigma weight residual 1.237 1.307 -0.070 1.13e-02 7.83e+03 3.85e+01 bond pdb=" C ASN A 413 " pdb=" O ASN A 413 " ideal model delta sigma weight residual 1.237 1.293 -0.056 1.19e-02 7.06e+03 2.23e+01 bond pdb=" C ASP A 412 " pdb=" O ASP A 412 " ideal model delta sigma weight residual 1.236 1.285 -0.049 1.15e-02 7.56e+03 1.78e+01 bond pdb=" C ARG A 406 " pdb=" O ARG A 406 " ideal model delta sigma weight residual 1.237 1.280 -0.043 1.19e-02 7.06e+03 1.32e+01 bond pdb=" N ILE A1019 " pdb=" CA ILE A1019 " ideal model delta sigma weight residual 1.456 1.496 -0.039 1.14e-02 7.69e+03 1.19e+01 ... (remaining 19404 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 26125 3.67 - 7.34: 126 7.34 - 11.01: 8 11.01 - 14.68: 1 14.68 - 18.35: 1 Bond angle restraints: 26261 Sorted by residual: angle pdb=" CA PRO A 416 " pdb=" N PRO A 416 " pdb=" CD PRO A 416 " ideal model delta sigma weight residual 112.00 93.65 18.35 1.40e+00 5.10e-01 1.72e+02 angle pdb=" C VAL A1947 " pdb=" N GLU A1948 " pdb=" CA GLU A1948 " ideal model delta sigma weight residual 121.54 132.77 -11.23 1.91e+00 2.74e-01 3.46e+01 angle pdb=" N VAL A1069 " pdb=" CA VAL A1069 " pdb=" C VAL A1069 " ideal model delta sigma weight residual 111.91 107.22 4.69 8.90e-01 1.26e+00 2.78e+01 angle pdb=" O LEU A1021 " pdb=" C LEU A1021 " pdb=" N LEU A1022 " ideal model delta sigma weight residual 122.09 127.29 -5.20 1.08e+00 8.57e-01 2.32e+01 angle pdb=" CA ASN A 415 " pdb=" C ASN A 415 " pdb=" N PRO A 416 " ideal model delta sigma weight residual 120.52 124.43 -3.91 8.30e-01 1.45e+00 2.21e+01 ... (remaining 26256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9886 17.95 - 35.90: 1332 35.90 - 53.85: 301 53.85 - 71.81: 68 71.81 - 89.76: 26 Dihedral angle restraints: 11613 sinusoidal: 4669 harmonic: 6944 Sorted by residual: dihedral pdb=" CA GLY A1028 " pdb=" C GLY A1028 " pdb=" N LEU A1029 " pdb=" CA LEU A1029 " ideal model delta harmonic sigma weight residual 180.00 92.75 87.25 0 5.00e+00 4.00e-02 3.04e+02 dihedral pdb=" CA PHE A1452 " pdb=" C PHE A1452 " pdb=" N ASN A1453 " pdb=" CA ASN A1453 " ideal model delta harmonic sigma weight residual 180.00 148.03 31.97 0 5.00e+00 4.00e-02 4.09e+01 dihedral pdb=" C ASN A1602 " pdb=" N ASN A1602 " pdb=" CA ASN A1602 " pdb=" CB ASN A1602 " ideal model delta harmonic sigma weight residual -122.60 -137.36 14.76 0 2.50e+00 1.60e-01 3.48e+01 ... (remaining 11610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2550 0.097 - 0.193: 326 0.193 - 0.290: 18 0.290 - 0.387: 2 0.387 - 0.484: 2 Chirality restraints: 2898 Sorted by residual: chirality pdb=" CA ASN A1602 " pdb=" N ASN A1602 " pdb=" C ASN A1602 " pdb=" CB ASN A1602 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" CA ASN A 419 " pdb=" N ASN A 419 " pdb=" C ASN A 419 " pdb=" CB ASN A 419 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA SER A 706 " pdb=" N SER A 706 " pdb=" C SER A 706 " pdb=" CB SER A 706 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 2895 not shown) Planarity restraints: 3394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 415 " 0.120 5.00e-02 4.00e+02 1.65e-01 4.37e+01 pdb=" N PRO A 416 " -0.285 5.00e-02 4.00e+02 pdb=" CA PRO A 416 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO A 416 " 0.090 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A2342 " 0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C GLY A2342 " -0.077 2.00e-02 2.50e+03 pdb=" O GLY A2342 " 0.029 2.00e-02 2.50e+03 pdb=" N SER A2343 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 413 " 0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C ASN A 413 " -0.070 2.00e-02 2.50e+03 pdb=" O ASN A 413 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU A 414 " 0.024 2.00e-02 2.50e+03 ... (remaining 3391 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 135 2.52 - 3.12: 14038 3.12 - 3.71: 28177 3.71 - 4.31: 42308 4.31 - 4.90: 69264 Nonbonded interactions: 153922 Sorted by model distance: nonbonded pdb=" CG PRO A1023 " pdb=" OH TYR A1649 " model vdw 1.925 3.440 nonbonded pdb=" O ASP A1534 " pdb=" OD1 ASP A1535 " model vdw 1.962 3.040 nonbonded pdb=" O LYS A1795 " pdb=" OG1 THR A1799 " model vdw 2.029 3.040 nonbonded pdb=" O ILE A1507 " pdb=" OD1 ASN A1598 " model vdw 2.031 3.040 nonbonded pdb=" OE2 GLU A 258 " pdb=" OH TYR A 407 " model vdw 2.163 3.040 ... (remaining 153917 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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 25.820 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.431 19413 Z= 0.532 Angle : 0.884 18.347 26261 Z= 0.585 Chirality : 0.062 0.484 2898 Planarity : 0.006 0.165 3394 Dihedral : 17.400 89.757 7167 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.74 % Favored : 94.00 % Rotamer: Outliers : 6.34 % Allowed : 17.18 % Favored : 76.48 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.79 % 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: -1.73 (0.16), residues: 2351 helix: 0.08 (0.20), residues: 664 sheet: -1.13 (0.22), residues: 453 loop : -1.87 (0.15), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1241 TYR 0.019 0.002 TYR A1646 PHE 0.016 0.002 PHE A 503 TRP 0.011 0.002 TRP A 102 HIS 0.005 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00751 (19409) covalent geometry : angle 0.88437 (26261) hydrogen bonds : bond 0.14813 ( 830) hydrogen bonds : angle 6.57421 ( 2232) metal coordination : bond 0.17488 ( 3) Misc. bond : bond 0.43130 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 200 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.6787 (tt0) cc_final: 0.6519 (tt0) REVERT: A 197 ASN cc_start: 0.7715 (t0) cc_final: 0.7485 (t0) REVERT: A 333 LYS cc_start: 0.8463 (ttpt) cc_final: 0.8257 (ttpt) REVERT: A 428 MET cc_start: 0.8629 (tpt) cc_final: 0.8392 (mmm) REVERT: A 651 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9246 (mm) REVERT: A 1327 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6843 (OUTLIER) REVERT: A 1462 TYR cc_start: 0.7125 (OUTLIER) cc_final: 0.5038 (p90) REVERT: A 1490 ASN cc_start: 0.7438 (p0) cc_final: 0.7042 (p0) REVERT: A 1496 ASN cc_start: 0.7331 (t0) cc_final: 0.6567 (m-40) REVERT: A 1499 MET cc_start: 0.6669 (tpp) cc_final: 0.5515 (ttp) REVERT: A 1576 LEU cc_start: 0.2556 (OUTLIER) cc_final: 0.1786 (mp) REVERT: A 1819 LEU cc_start: 0.8442 (mt) cc_final: 0.8229 (mt) REVERT: A 1955 GLU cc_start: 0.5589 (OUTLIER) cc_final: 0.5352 (mp0) REVERT: A 2181 ASN cc_start: 0.1215 (OUTLIER) cc_final: -0.0697 (m-40) outliers start: 135 outliers final: 77 residues processed: 320 average time/residue: 0.5278 time to fit residues: 194.7619 Evaluate side-chains 211 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 129 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 879 ASP Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1285 THR Chi-restraints excluded: chain A residue 1297 SER Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1392 TYR Chi-restraints excluded: chain A residue 1433 CYS Chi-restraints excluded: chain A residue 1462 TYR Chi-restraints excluded: chain A residue 1515 ASP Chi-restraints excluded: chain A residue 1543 THR Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1598 ASN Chi-restraints excluded: chain A residue 1602 ASN Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1671 SER Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1776 THR Chi-restraints excluded: chain A residue 1801 SER Chi-restraints excluded: chain A residue 1814 PHE Chi-restraints excluded: chain A residue 1821 ASN Chi-restraints excluded: chain A residue 1870 THR Chi-restraints excluded: chain A residue 1902 THR Chi-restraints excluded: chain A residue 1914 THR Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1955 GLU Chi-restraints excluded: chain A residue 1963 THR Chi-restraints excluded: chain A residue 1988 THR Chi-restraints excluded: chain A residue 1992 THR Chi-restraints excluded: chain A residue 1995 ASP Chi-restraints excluded: chain A residue 2005 VAL Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2181 ASN Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2259 ASN Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN A 8 GLN A 380 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 GLN A 732 GLN A 741 GLN A 795 HIS A 876 ASN A 941 ASN A 949 ASN A 988 GLN A1109 ASN ** A1257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1390 ASN A1584 ASN A1593 ASN A1621 GLN A1631 ASN A1724 ASN A1763 GLN A2058 ASN A2143 GLN ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2319 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.196921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.121286 restraints weight = 27248.356| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.89 r_work: 0.2986 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19413 Z= 0.159 Angle : 0.591 9.513 26261 Z= 0.322 Chirality : 0.047 0.182 2898 Planarity : 0.004 0.096 3394 Dihedral : 7.484 73.691 2670 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.19 % Rotamer: Outliers : 4.32 % Allowed : 20.75 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.62 (0.17), residues: 2351 helix: 1.36 (0.20), residues: 663 sheet: -0.67 (0.22), residues: 466 loop : -1.33 (0.16), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1241 TYR 0.015 0.001 TYR A 990 PHE 0.017 0.001 PHE A 937 TRP 0.021 0.001 TRP A1949 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd covalent geometry : bond 0.00366 (19409) covalent geometry : angle 0.59069 (26261) hydrogen bonds : bond 0.05543 ( 830) hydrogen bonds : angle 5.10038 ( 2232) metal coordination : bond 0.00618 ( 3) Misc. bond : bond 0.00737 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 148 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 THR cc_start: 0.8983 (p) cc_final: 0.8762 (t) REVERT: A 333 LYS cc_start: 0.9002 (ttpt) cc_final: 0.8797 (tmmt) REVERT: A 520 TRP cc_start: 0.8214 (m-10) cc_final: 0.7848 (m100) REVERT: A 535 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8812 (mtmm) REVERT: A 646 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.8872 (tp) REVERT: A 751 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8423 (mttm) REVERT: A 760 LYS cc_start: 0.9144 (mttt) cc_final: 0.8799 (mmtp) REVERT: A 1020 ASP cc_start: 0.7928 (p0) cc_final: 0.7685 (p0) REVERT: A 1027 GLU cc_start: 0.7787 (tt0) cc_final: 0.7207 (tm-30) REVERT: A 1212 LYS cc_start: 0.0784 (OUTLIER) cc_final: 0.0524 (mmtm) REVERT: A 1230 PHE cc_start: 0.0263 (OUTLIER) cc_final: -0.0205 (m-80) REVERT: A 1302 VAL cc_start: 0.5365 (OUTLIER) cc_final: 0.4692 (p) REVERT: A 1327 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5907 (tp) REVERT: A 1332 MET cc_start: 0.4433 (pmm) cc_final: 0.0994 (ttp) REVERT: A 1462 TYR cc_start: 0.6912 (OUTLIER) cc_final: 0.3763 (p90) REVERT: A 1470 LYS cc_start: 0.7997 (ttmt) cc_final: 0.7632 (mtmt) REVERT: A 1477 TYR cc_start: 0.7637 (t80) cc_final: 0.6887 (t80) REVERT: A 1490 ASN cc_start: 0.7327 (p0) cc_final: 0.6988 (p0) REVERT: A 1499 MET cc_start: 0.6696 (tpp) cc_final: 0.5325 (ttp) REVERT: A 1567 LYS cc_start: 0.9143 (ttmt) cc_final: 0.8664 (ttpm) REVERT: A 1576 LEU cc_start: 0.2905 (OUTLIER) cc_final: 0.2213 (mp) REVERT: A 1590 ASN cc_start: 0.8606 (m-40) cc_final: 0.8360 (m110) REVERT: A 2006 MET cc_start: 0.4348 (tpt) cc_final: 0.2726 (ttt) outliers start: 92 outliers final: 42 residues processed: 235 average time/residue: 0.5464 time to fit residues: 146.9510 Evaluate side-chains 182 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 131 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 751 LYS Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 874 HIS Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1212 LYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1230 PHE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1462 TYR Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1626 CYS Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1776 THR Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1895 LEU Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 1988 THR Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 145 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 205 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 413 ASN A 487 ASN ** A1257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1580 ASN A1633 GLN A1724 ASN A2058 ASN A2260 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.195402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.118421 restraints weight = 27348.521| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.85 r_work: 0.2926 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19413 Z= 0.186 Angle : 0.588 8.136 26261 Z= 0.320 Chirality : 0.047 0.176 2898 Planarity : 0.004 0.096 3394 Dihedral : 6.337 58.549 2590 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.04 % Allowed : 22.21 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.31 (0.17), residues: 2351 helix: 1.64 (0.20), residues: 661 sheet: -0.53 (0.23), residues: 465 loop : -1.12 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2118 TYR 0.015 0.002 TYR A1646 PHE 0.028 0.002 PHE A 937 TRP 0.010 0.001 TRP A 118 HIS 0.006 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00445 (19409) covalent geometry : angle 0.58821 (26261) hydrogen bonds : bond 0.05824 ( 830) hydrogen bonds : angle 4.97863 ( 2232) metal coordination : bond 0.01069 ( 3) Misc. bond : bond 0.00588 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 141 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8336 (t0) REVERT: A 333 LYS cc_start: 0.8938 (ttpt) cc_final: 0.8587 (ttpt) REVERT: A 520 TRP cc_start: 0.8133 (m-10) cc_final: 0.7844 (m100) REVERT: A 543 LEU cc_start: 0.8141 (mt) cc_final: 0.7893 (mt) REVERT: A 646 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.8780 (tp) REVERT: A 814 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7515 (p0) REVERT: A 897 ARG cc_start: 0.6387 (OUTLIER) cc_final: 0.5834 (ptm160) REVERT: A 1027 GLU cc_start: 0.7642 (tt0) cc_final: 0.7100 (tm-30) REVERT: A 1029 LEU cc_start: 0.7434 (tp) cc_final: 0.7168 (tp) REVERT: A 1212 LYS cc_start: 0.0571 (OUTLIER) cc_final: 0.0354 (mmtm) REVERT: A 1230 PHE cc_start: -0.0075 (OUTLIER) cc_final: -0.0504 (m-80) REVERT: A 1302 VAL cc_start: 0.5277 (OUTLIER) cc_final: 0.4618 (p) REVERT: A 1332 MET cc_start: 0.4978 (pmm) cc_final: 0.1300 (ttp) REVERT: A 1462 TYR cc_start: 0.6923 (OUTLIER) cc_final: 0.3348 (p90) REVERT: A 1470 LYS cc_start: 0.7897 (ttmt) cc_final: 0.7402 (mtmm) REVERT: A 1477 TYR cc_start: 0.7606 (t80) cc_final: 0.6869 (t80) REVERT: A 1484 PHE cc_start: 0.8452 (m-80) cc_final: 0.8124 (m-80) REVERT: A 1490 ASN cc_start: 0.7326 (p0) cc_final: 0.7005 (p0) REVERT: A 1567 LYS cc_start: 0.9091 (ttmt) cc_final: 0.8801 (tttm) REVERT: A 1576 LEU cc_start: 0.2735 (OUTLIER) cc_final: 0.2082 (mp) REVERT: A 1788 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8822 (mttp) REVERT: A 2006 MET cc_start: 0.4394 (tpt) cc_final: 0.2769 (ttt) outliers start: 86 outliers final: 45 residues processed: 219 average time/residue: 0.5117 time to fit residues: 129.1765 Evaluate side-chains 177 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 122 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 897 ARG Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1212 LYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1230 PHE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1462 TYR Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1626 CYS Chi-restraints excluded: chain A residue 1650 VAL Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1776 THR Chi-restraints excluded: chain A residue 1788 LYS Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1895 LEU Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1988 THR Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2361 VAL Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 181 optimal weight: 1.9990 chunk 150 optimal weight: 0.0970 chunk 20 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 166 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 487 ASN A1257 HIS A1530 ASN A1580 ASN A1724 ASN A2058 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.196937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120550 restraints weight = 27260.635| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.78 r_work: 0.2996 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19413 Z= 0.129 Angle : 0.537 8.924 26261 Z= 0.291 Chirality : 0.046 0.181 2898 Planarity : 0.004 0.091 3394 Dihedral : 5.764 58.657 2578 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.46 % Allowed : 21.78 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.03 (0.17), residues: 2351 helix: 1.98 (0.20), residues: 663 sheet: -0.36 (0.23), residues: 472 loop : -0.94 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1495 TYR 0.014 0.001 TYR A1646 PHE 0.026 0.001 PHE A1474 TRP 0.010 0.001 TRP A 118 HIS 0.003 0.001 HIS A 924 Details of bonding type rmsd covalent geometry : bond 0.00293 (19409) covalent geometry : angle 0.53750 (26261) hydrogen bonds : bond 0.04720 ( 830) hydrogen bonds : angle 4.72543 ( 2232) metal coordination : bond 0.00643 ( 3) Misc. bond : bond 0.00557 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 138 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8330 (tpt) cc_final: 0.8025 (tpt) REVERT: A 197 ASN cc_start: 0.7591 (m-40) cc_final: 0.6886 (t0) REVERT: A 201 ILE cc_start: 0.8661 (pt) cc_final: 0.8407 (mt) REVERT: A 227 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8165 (mt-10) REVERT: A 238 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.7869 (m-40) REVERT: A 333 LYS cc_start: 0.8874 (ttpt) cc_final: 0.8274 (mtpp) REVERT: A 520 TRP cc_start: 0.8269 (m-10) cc_final: 0.7920 (m100) REVERT: A 543 LEU cc_start: 0.8045 (mt) cc_final: 0.7806 (mt) REVERT: A 646 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.8796 (tp) REVERT: A 814 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7476 (p0) REVERT: A 897 ARG cc_start: 0.6402 (OUTLIER) cc_final: 0.5863 (ptm160) REVERT: A 1027 GLU cc_start: 0.7783 (tt0) cc_final: 0.7392 (tm-30) REVERT: A 1029 LEU cc_start: 0.7461 (tp) cc_final: 0.7201 (tp) REVERT: A 1230 PHE cc_start: 0.0145 (OUTLIER) cc_final: -0.0429 (m-80) REVERT: A 1302 VAL cc_start: 0.5608 (OUTLIER) cc_final: 0.4998 (p) REVERT: A 1332 MET cc_start: 0.4436 (pmm) cc_final: 0.0759 (ttp) REVERT: A 1390 ASN cc_start: 0.5810 (OUTLIER) cc_final: 0.5420 (t0) REVERT: A 1462 TYR cc_start: 0.6929 (OUTLIER) cc_final: 0.3773 (p90) REVERT: A 1470 LYS cc_start: 0.7994 (ttmt) cc_final: 0.7652 (mtmt) REVERT: A 1477 TYR cc_start: 0.7574 (t80) cc_final: 0.6888 (t80) REVERT: A 1490 ASN cc_start: 0.7388 (p0) cc_final: 0.7060 (p0) REVERT: A 1495 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7841 (mmm-85) REVERT: A 1499 MET cc_start: 0.6906 (tpp) cc_final: 0.5589 (ttp) REVERT: A 1567 LYS cc_start: 0.9157 (ttmt) cc_final: 0.8704 (ttpm) REVERT: A 1775 ASP cc_start: 0.4852 (OUTLIER) cc_final: 0.3751 (m-30) REVERT: A 1985 ILE cc_start: 0.5977 (OUTLIER) cc_final: 0.5754 (mp) REVERT: A 2006 MET cc_start: 0.4355 (tpt) cc_final: 0.2697 (ttt) outliers start: 95 outliers final: 43 residues processed: 219 average time/residue: 0.4681 time to fit residues: 119.5621 Evaluate side-chains 178 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 125 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 874 HIS Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 897 ARG Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1230 PHE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1328 SER Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1390 ASN Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1462 TYR Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1626 CYS Chi-restraints excluded: chain A residue 1650 VAL Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1775 ASP Chi-restraints excluded: chain A residue 1776 THR Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 1988 THR Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 38 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 183 optimal weight: 0.5980 chunk 107 optimal weight: 8.9990 chunk 122 optimal weight: 40.0000 chunk 117 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 145 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 231 optimal weight: 30.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 487 ASN A1580 ASN A1584 ASN A1593 ASN A1724 ASN A2058 ASN A2143 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.194830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.117317 restraints weight = 27319.352| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.78 r_work: 0.2929 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19413 Z= 0.205 Angle : 0.592 10.204 26261 Z= 0.319 Chirality : 0.048 0.210 2898 Planarity : 0.004 0.090 3394 Dihedral : 5.698 55.658 2570 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.27 % Allowed : 22.49 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.05 (0.17), residues: 2351 helix: 1.83 (0.20), residues: 662 sheet: -0.42 (0.23), residues: 475 loop : -0.92 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1495 TYR 0.016 0.002 TYR A 990 PHE 0.029 0.002 PHE A1474 TRP 0.010 0.001 TRP A 118 HIS 0.004 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00497 (19409) covalent geometry : angle 0.59182 (26261) hydrogen bonds : bond 0.05897 ( 830) hydrogen bonds : angle 4.88876 ( 2232) metal coordination : bond 0.01199 ( 3) Misc. bond : bond 0.00546 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 127 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8291 (tpt) cc_final: 0.7978 (tpt) REVERT: A 2 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8407 (t0) REVERT: A 197 ASN cc_start: 0.7684 (m-40) cc_final: 0.7057 (t0) REVERT: A 520 TRP cc_start: 0.8229 (m-10) cc_final: 0.7965 (m100) REVERT: A 543 LEU cc_start: 0.8139 (mt) cc_final: 0.7857 (mt) REVERT: A 646 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.8808 (tp) REVERT: A 751 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8500 (mttm) REVERT: A 814 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7677 (p0) REVERT: A 897 ARG cc_start: 0.6430 (OUTLIER) cc_final: 0.5767 (ptm160) REVERT: A 1027 GLU cc_start: 0.7867 (tt0) cc_final: 0.7504 (tm-30) REVERT: A 1230 PHE cc_start: 0.0170 (OUTLIER) cc_final: -0.0430 (m-80) REVERT: A 1302 VAL cc_start: 0.5472 (OUTLIER) cc_final: 0.4860 (p) REVERT: A 1390 ASN cc_start: 0.6351 (OUTLIER) cc_final: 0.6010 (t0) REVERT: A 1462 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.3818 (p90) REVERT: A 1470 LYS cc_start: 0.8007 (ttmt) cc_final: 0.7646 (mtmt) REVERT: A 1477 TYR cc_start: 0.7603 (t80) cc_final: 0.6913 (t80) REVERT: A 1490 ASN cc_start: 0.7427 (p0) cc_final: 0.7112 (p0) REVERT: A 1495 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.7978 (mmm-85) REVERT: A 1499 MET cc_start: 0.6782 (tpp) cc_final: 0.5495 (ttp) REVERT: A 1906 LEU cc_start: 0.7925 (mm) cc_final: 0.7596 (mp) REVERT: A 1917 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6380 (tm-30) REVERT: A 1985 ILE cc_start: 0.5966 (OUTLIER) cc_final: 0.5741 (mp) REVERT: A 2006 MET cc_start: 0.4383 (tpt) cc_final: 0.2807 (ttt) outliers start: 91 outliers final: 54 residues processed: 207 average time/residue: 0.4836 time to fit residues: 116.0598 Evaluate side-chains 187 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 122 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 751 LYS Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 897 ARG Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1230 PHE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1264 TRP Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1328 SER Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1390 ASN Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1443 ILE Chi-restraints excluded: chain A residue 1462 TYR Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1626 CYS Chi-restraints excluded: chain A residue 1650 VAL Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1776 THR Chi-restraints excluded: chain A residue 1779 ASP Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1917 GLU Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 1988 THR Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2361 VAL Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 189 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 198 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A1580 ASN A1724 ASN A2058 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.197421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122142 restraints weight = 27191.155| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.99 r_work: 0.3017 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19413 Z= 0.117 Angle : 0.521 10.394 26261 Z= 0.281 Chirality : 0.045 0.193 2898 Planarity : 0.004 0.089 3394 Dihedral : 5.344 58.895 2570 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.13 % Allowed : 22.77 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.26 (0.17), residues: 2351 helix: 2.17 (0.20), residues: 662 sheet: -0.26 (0.23), residues: 485 loop : -0.78 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1495 TYR 0.013 0.001 TYR A1646 PHE 0.030 0.001 PHE A1474 TRP 0.009 0.001 TRP A 118 HIS 0.003 0.001 HIS A 924 Details of bonding type rmsd covalent geometry : bond 0.00264 (19409) covalent geometry : angle 0.52091 (26261) hydrogen bonds : bond 0.04343 ( 830) hydrogen bonds : angle 4.62086 ( 2232) metal coordination : bond 0.00531 ( 3) Misc. bond : bond 0.00530 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 137 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8302 (tpt) cc_final: 0.7991 (tpt) REVERT: A 197 ASN cc_start: 0.7543 (m-40) cc_final: 0.6912 (t0) REVERT: A 201 ILE cc_start: 0.8561 (pt) cc_final: 0.8345 (mt) REVERT: A 279 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7560 (mt-10) REVERT: A 333 LYS cc_start: 0.8720 (tmmt) cc_final: 0.8261 (mmtt) REVERT: A 520 TRP cc_start: 0.8210 (m-10) cc_final: 0.7909 (m100) REVERT: A 543 LEU cc_start: 0.8050 (mt) cc_final: 0.7732 (mt) REVERT: A 646 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.8793 (tp) REVERT: A 751 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8446 (mttm) REVERT: A 814 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7417 (p0) REVERT: A 897 ARG cc_start: 0.6414 (OUTLIER) cc_final: 0.5773 (ptm160) REVERT: A 1230 PHE cc_start: 0.0118 (OUTLIER) cc_final: -0.0465 (m-80) REVERT: A 1332 MET cc_start: 0.4307 (pmm) cc_final: 0.0758 (ttp) REVERT: A 1390 ASN cc_start: 0.5916 (OUTLIER) cc_final: 0.5406 (t0) REVERT: A 1391 PHE cc_start: 0.6699 (OUTLIER) cc_final: 0.5885 (p90) REVERT: A 1462 TYR cc_start: 0.7117 (OUTLIER) cc_final: 0.3973 (p90) REVERT: A 1470 LYS cc_start: 0.7988 (ttmt) cc_final: 0.7543 (mtmm) REVERT: A 1477 TYR cc_start: 0.7579 (t80) cc_final: 0.6950 (t80) REVERT: A 1490 ASN cc_start: 0.7328 (p0) cc_final: 0.7003 (p0) REVERT: A 1495 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7706 (mmm-85) REVERT: A 1499 MET cc_start: 0.6566 (tpp) cc_final: 0.5248 (ttp) REVERT: A 1567 LYS cc_start: 0.9157 (ttmt) cc_final: 0.8686 (ttpm) REVERT: A 1641 ILE cc_start: 0.8489 (mt) cc_final: 0.8237 (mt) REVERT: A 1775 ASP cc_start: 0.4591 (OUTLIER) cc_final: 0.3476 (m-30) REVERT: A 1906 LEU cc_start: 0.7909 (mm) cc_final: 0.7641 (mp) REVERT: A 1917 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6366 (tm-30) REVERT: A 2006 MET cc_start: 0.4218 (tpt) cc_final: 0.2633 (ttt) REVERT: A 2289 MET cc_start: -0.0348 (tpt) cc_final: -0.2419 (ptm) outliers start: 88 outliers final: 48 residues processed: 210 average time/residue: 0.5220 time to fit residues: 126.9803 Evaluate side-chains 185 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 127 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 751 LYS Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 874 HIS Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 897 ARG Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1230 PHE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1264 TRP Chi-restraints excluded: chain A residue 1328 SER Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1390 ASN Chi-restraints excluded: chain A residue 1391 PHE Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1462 TYR Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1626 CYS Chi-restraints excluded: chain A residue 1650 VAL Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1775 ASP Chi-restraints excluded: chain A residue 1776 THR Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1917 GLU Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1988 THR Chi-restraints excluded: chain A residue 1992 THR Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2361 VAL Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 47 optimal weight: 0.5980 chunk 152 optimal weight: 0.6980 chunk 196 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 226 optimal weight: 0.6980 chunk 204 optimal weight: 8.9990 chunk 201 optimal weight: 0.3980 chunk 210 optimal weight: 20.0000 chunk 162 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN A 487 ASN A 972 ASN A1580 ASN A1724 ASN A1931 ASN A2058 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.198969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.120097 restraints weight = 27369.004| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.38 r_work: 0.3031 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 19413 Z= 0.104 Angle : 0.510 9.974 26261 Z= 0.274 Chirality : 0.045 0.171 2898 Planarity : 0.004 0.086 3394 Dihedral : 5.037 54.733 2569 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.38 % Allowed : 23.99 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.47 (0.18), residues: 2351 helix: 2.34 (0.20), residues: 664 sheet: -0.12 (0.23), residues: 483 loop : -0.66 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1495 TYR 0.019 0.001 TYR A 990 PHE 0.031 0.001 PHE A1474 TRP 0.008 0.001 TRP A 118 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd covalent geometry : bond 0.00228 (19409) covalent geometry : angle 0.50986 (26261) hydrogen bonds : bond 0.03862 ( 830) hydrogen bonds : angle 4.45680 ( 2232) metal coordination : bond 0.00394 ( 3) Misc. bond : bond 0.00528 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 142 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8321 (tpt) cc_final: 0.8001 (tpt) REVERT: A 201 ILE cc_start: 0.8536 (pt) cc_final: 0.8309 (mt) REVERT: A 279 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7594 (mt-10) REVERT: A 333 LYS cc_start: 0.8775 (tmmt) cc_final: 0.8231 (mmtt) REVERT: A 520 TRP cc_start: 0.8241 (m-10) cc_final: 0.7967 (m100) REVERT: A 543 LEU cc_start: 0.7989 (mt) cc_final: 0.7670 (mt) REVERT: A 646 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8780 (tp) REVERT: A 751 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8434 (mttm) REVERT: A 1025 LEU cc_start: 0.9070 (mt) cc_final: 0.8793 (mp) REVERT: A 1230 PHE cc_start: 0.0029 (OUTLIER) cc_final: -0.0501 (m-80) REVERT: A 1332 MET cc_start: 0.4396 (pmm) cc_final: 0.0718 (ttp) REVERT: A 1390 ASN cc_start: 0.5623 (OUTLIER) cc_final: 0.5113 (t0) REVERT: A 1391 PHE cc_start: 0.6592 (OUTLIER) cc_final: 0.5855 (p90) REVERT: A 1462 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.3814 (p90) REVERT: A 1470 LYS cc_start: 0.7925 (ttmt) cc_final: 0.7506 (mtmm) REVERT: A 1477 TYR cc_start: 0.7589 (t80) cc_final: 0.6969 (t80) REVERT: A 1490 ASN cc_start: 0.7317 (p0) cc_final: 0.7002 (p0) REVERT: A 1495 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7799 (mmm-85) REVERT: A 1499 MET cc_start: 0.6458 (tpp) cc_final: 0.5149 (ttp) REVERT: A 1567 LYS cc_start: 0.9160 (ttmt) cc_final: 0.8717 (ttpm) REVERT: A 1641 ILE cc_start: 0.8492 (mt) cc_final: 0.8238 (mt) REVERT: A 1906 LEU cc_start: 0.7801 (mm) cc_final: 0.7561 (mp) REVERT: A 1927 ILE cc_start: 0.6044 (OUTLIER) cc_final: 0.5714 (pp) REVERT: A 1947 VAL cc_start: 0.6423 (OUTLIER) cc_final: 0.6188 (m) REVERT: A 2006 MET cc_start: 0.4133 (tpt) cc_final: 0.2627 (ttt) REVERT: A 2289 MET cc_start: -0.0126 (tpt) cc_final: -0.1909 (ptm) outliers start: 72 outliers final: 37 residues processed: 201 average time/residue: 0.4776 time to fit residues: 111.5891 Evaluate side-chains 177 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 751 LYS Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 874 HIS Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1230 PHE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1264 TRP Chi-restraints excluded: chain A residue 1328 SER Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1390 ASN Chi-restraints excluded: chain A residue 1391 PHE Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1462 TYR Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1626 CYS Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1807 ASP Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1988 THR Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2320 TYR Chi-restraints excluded: chain A residue 2361 VAL Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 145 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 114 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A1724 ASN A2058 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.198246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.121864 restraints weight = 27330.225| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.83 r_work: 0.3023 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19413 Z= 0.113 Angle : 0.517 9.491 26261 Z= 0.277 Chirality : 0.045 0.161 2898 Planarity : 0.004 0.085 3394 Dihedral : 4.836 50.808 2563 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.10 % Allowed : 24.32 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.55 (0.18), residues: 2351 helix: 2.38 (0.20), residues: 664 sheet: -0.04 (0.23), residues: 481 loop : -0.60 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1495 TYR 0.022 0.001 TYR A1459 PHE 0.033 0.001 PHE A1474 TRP 0.009 0.001 TRP A 118 HIS 0.003 0.001 HIS A 924 Details of bonding type rmsd covalent geometry : bond 0.00254 (19409) covalent geometry : angle 0.51717 (26261) hydrogen bonds : bond 0.04141 ( 830) hydrogen bonds : angle 4.46779 ( 2232) metal coordination : bond 0.00536 ( 3) Misc. bond : bond 0.00543 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 137 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8333 (tpt) cc_final: 0.8017 (tpt) REVERT: A 201 ILE cc_start: 0.8532 (pt) cc_final: 0.8318 (mt) REVERT: A 227 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8178 (mt-10) REVERT: A 279 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7654 (mt-10) REVERT: A 333 LYS cc_start: 0.8758 (tmmt) cc_final: 0.8343 (mtmm) REVERT: A 520 TRP cc_start: 0.8253 (m-10) cc_final: 0.7973 (m100) REVERT: A 543 LEU cc_start: 0.7972 (mt) cc_final: 0.7691 (mt) REVERT: A 570 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.8253 (mmt) REVERT: A 646 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8760 (tp) REVERT: A 751 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8365 (mttm) REVERT: A 814 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7331 (p0) REVERT: A 1212 LYS cc_start: 0.1097 (OUTLIER) cc_final: 0.0875 (mmtm) REVERT: A 1230 PHE cc_start: 0.0081 (OUTLIER) cc_final: -0.0490 (m-80) REVERT: A 1327 LEU cc_start: 0.6286 (OUTLIER) cc_final: 0.6045 (tp) REVERT: A 1332 MET cc_start: 0.4479 (pmm) cc_final: 0.0886 (ttp) REVERT: A 1390 ASN cc_start: 0.5475 (OUTLIER) cc_final: 0.4933 (t0) REVERT: A 1391 PHE cc_start: 0.6510 (OUTLIER) cc_final: 0.5824 (p90) REVERT: A 1462 TYR cc_start: 0.7128 (OUTLIER) cc_final: 0.3795 (p90) REVERT: A 1470 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7528 (mtmm) REVERT: A 1477 TYR cc_start: 0.7632 (t80) cc_final: 0.7011 (t80) REVERT: A 1490 ASN cc_start: 0.7212 (p0) cc_final: 0.6926 (p0) REVERT: A 1495 ARG cc_start: 0.8074 (ttm-80) cc_final: 0.7781 (mmm-85) REVERT: A 1499 MET cc_start: 0.6388 (tpp) cc_final: 0.5025 (ttp) REVERT: A 1567 LYS cc_start: 0.9158 (ttmt) cc_final: 0.8715 (ttpm) REVERT: A 1641 ILE cc_start: 0.8511 (mt) cc_final: 0.8243 (mt) REVERT: A 1775 ASP cc_start: 0.4313 (OUTLIER) cc_final: 0.3252 (m-30) REVERT: A 1906 LEU cc_start: 0.7790 (mm) cc_final: 0.7575 (mp) REVERT: A 1927 ILE cc_start: 0.6171 (OUTLIER) cc_final: 0.5834 (pp) REVERT: A 1947 VAL cc_start: 0.6355 (OUTLIER) cc_final: 0.6111 (m) REVERT: A 2006 MET cc_start: 0.3957 (tpt) cc_final: 0.2687 (ttt) REVERT: A 2289 MET cc_start: -0.0151 (tpt) cc_final: -0.2133 (ptm) outliers start: 66 outliers final: 40 residues processed: 197 average time/residue: 0.4673 time to fit residues: 107.2584 Evaluate side-chains 178 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 125 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 751 LYS Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1212 LYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1230 PHE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1264 TRP Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1328 SER Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1390 ASN Chi-restraints excluded: chain A residue 1391 PHE Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1462 TYR Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1626 CYS Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1775 ASP Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1988 THR Chi-restraints excluded: chain A residue 1992 THR Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2320 TYR Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2361 VAL Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 194 optimal weight: 0.0570 chunk 97 optimal weight: 0.9990 chunk 140 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A1445 GLN A1724 ASN A2001 ASN A2058 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.198233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122189 restraints weight = 27223.229| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.62 r_work: 0.3041 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19413 Z= 0.117 Angle : 0.523 11.255 26261 Z= 0.281 Chirality : 0.045 0.170 2898 Planarity : 0.004 0.084 3394 Dihedral : 4.770 49.398 2563 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.62 % Rotamer: Outliers : 3.24 % Allowed : 24.04 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.57 (0.18), residues: 2351 helix: 2.38 (0.20), residues: 664 sheet: -0.03 (0.23), residues: 485 loop : -0.59 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1495 TYR 0.013 0.001 TYR A1646 PHE 0.033 0.001 PHE A1474 TRP 0.009 0.001 TRP A 118 HIS 0.003 0.001 HIS A1456 Details of bonding type rmsd covalent geometry : bond 0.00265 (19409) covalent geometry : angle 0.52297 (26261) hydrogen bonds : bond 0.04225 ( 830) hydrogen bonds : angle 4.45787 ( 2232) metal coordination : bond 0.00555 ( 3) Misc. bond : bond 0.00506 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 135 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8323 (tpt) cc_final: 0.8013 (tpt) REVERT: A 333 LYS cc_start: 0.8734 (tmmt) cc_final: 0.8258 (mmtt) REVERT: A 520 TRP cc_start: 0.8201 (m-10) cc_final: 0.7903 (m100) REVERT: A 543 LEU cc_start: 0.8007 (mt) cc_final: 0.7688 (mt) REVERT: A 570 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8238 (mmt) REVERT: A 613 GLU cc_start: 0.7900 (pm20) cc_final: 0.7650 (mp0) REVERT: A 646 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8751 (tp) REVERT: A 651 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9099 (mm) REVERT: A 751 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8344 (mttm) REVERT: A 814 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7325 (p0) REVERT: A 1212 LYS cc_start: 0.1248 (OUTLIER) cc_final: 0.0981 (mmtm) REVERT: A 1230 PHE cc_start: 0.0185 (OUTLIER) cc_final: -0.0492 (m-80) REVERT: A 1327 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6231 (tp) REVERT: A 1390 ASN cc_start: 0.5828 (OUTLIER) cc_final: 0.5297 (t0) REVERT: A 1391 PHE cc_start: 0.6610 (OUTLIER) cc_final: 0.5850 (p90) REVERT: A 1470 LYS cc_start: 0.7959 (ttmt) cc_final: 0.7553 (mtmm) REVERT: A 1477 TYR cc_start: 0.7573 (t80) cc_final: 0.6994 (t80) REVERT: A 1490 ASN cc_start: 0.7204 (p0) cc_final: 0.6922 (p0) REVERT: A 1495 ARG cc_start: 0.8053 (ttm-80) cc_final: 0.7736 (mmm-85) REVERT: A 1499 MET cc_start: 0.6617 (tpp) cc_final: 0.5304 (ttp) REVERT: A 1567 LYS cc_start: 0.9149 (ttmt) cc_final: 0.8705 (ttpm) REVERT: A 1641 ILE cc_start: 0.8455 (mt) cc_final: 0.8184 (mt) REVERT: A 1906 LEU cc_start: 0.7784 (mm) cc_final: 0.7567 (mp) REVERT: A 1927 ILE cc_start: 0.6380 (OUTLIER) cc_final: 0.6079 (pp) REVERT: A 1947 VAL cc_start: 0.6247 (OUTLIER) cc_final: 0.5997 (m) REVERT: A 2006 MET cc_start: 0.3978 (tpt) cc_final: 0.2686 (ttt) REVERT: A 2289 MET cc_start: -0.0047 (tpt) cc_final: -0.2029 (ptm) outliers start: 69 outliers final: 47 residues processed: 196 average time/residue: 0.4846 time to fit residues: 110.6376 Evaluate side-chains 185 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 126 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 751 LYS Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1212 LYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1230 PHE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1264 TRP Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1328 SER Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1390 ASN Chi-restraints excluded: chain A residue 1391 PHE Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1462 TYR Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1626 CYS Chi-restraints excluded: chain A residue 1650 VAL Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1988 THR Chi-restraints excluded: chain A residue 1992 THR Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2320 TYR Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2361 VAL Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 73 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 189 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 200 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1724 ASN A2058 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.199263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.120620 restraints weight = 27347.058| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.47 r_work: 0.3019 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19413 Z= 0.104 Angle : 0.515 11.562 26261 Z= 0.276 Chirality : 0.045 0.181 2898 Planarity : 0.004 0.084 3394 Dihedral : 4.661 49.603 2563 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.87 % Favored : 96.09 % Rotamer: Outliers : 2.58 % Allowed : 24.98 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.64 (0.18), residues: 2351 helix: 2.42 (0.20), residues: 666 sheet: 0.07 (0.23), residues: 484 loop : -0.56 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1495 TYR 0.018 0.001 TYR A 990 PHE 0.032 0.001 PHE A1474 TRP 0.008 0.001 TRP A 118 HIS 0.003 0.001 HIS A 924 Details of bonding type rmsd covalent geometry : bond 0.00229 (19409) covalent geometry : angle 0.51505 (26261) hydrogen bonds : bond 0.03865 ( 830) hydrogen bonds : angle 4.39282 ( 2232) metal coordination : bond 0.00419 ( 3) Misc. bond : bond 0.00501 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 132 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8345 (tpt) cc_final: 0.8023 (tpt) REVERT: A 227 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8244 (mt-10) REVERT: A 333 LYS cc_start: 0.8720 (tmmt) cc_final: 0.8194 (mmtt) REVERT: A 520 TRP cc_start: 0.8252 (m-10) cc_final: 0.7930 (m100) REVERT: A 543 LEU cc_start: 0.7928 (mt) cc_final: 0.7626 (mt) REVERT: A 570 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8205 (mmt) REVERT: A 646 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.8801 (tp) REVERT: A 751 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8418 (mttm) REVERT: A 814 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7514 (p0) REVERT: A 1212 LYS cc_start: 0.1076 (OUTLIER) cc_final: 0.0823 (mmtm) REVERT: A 1230 PHE cc_start: 0.0164 (OUTLIER) cc_final: -0.0463 (m-80) REVERT: A 1332 MET cc_start: 0.4090 (pmm) cc_final: 0.0359 (mtm) REVERT: A 1390 ASN cc_start: 0.5622 (OUTLIER) cc_final: 0.5087 (t0) REVERT: A 1391 PHE cc_start: 0.6596 (OUTLIER) cc_final: 0.5845 (p90) REVERT: A 1470 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7593 (mtmm) REVERT: A 1477 TYR cc_start: 0.7603 (t80) cc_final: 0.7031 (t80) REVERT: A 1490 ASN cc_start: 0.7170 (p0) cc_final: 0.6903 (p0) REVERT: A 1495 ARG cc_start: 0.8111 (ttm-80) cc_final: 0.7792 (mmm-85) REVERT: A 1499 MET cc_start: 0.6632 (tpp) cc_final: 0.5348 (ttp) REVERT: A 1567 LYS cc_start: 0.9171 (ttmt) cc_final: 0.8745 (ttpm) REVERT: A 1592 LYS cc_start: 0.7984 (tppt) cc_final: 0.7518 (tppt) REVERT: A 1641 ILE cc_start: 0.8484 (mt) cc_final: 0.8208 (mt) REVERT: A 1906 LEU cc_start: 0.7825 (mm) cc_final: 0.7615 (mp) REVERT: A 1927 ILE cc_start: 0.6310 (OUTLIER) cc_final: 0.5997 (pp) REVERT: A 1947 VAL cc_start: 0.6208 (OUTLIER) cc_final: 0.5941 (m) REVERT: A 1973 ILE cc_start: 0.5687 (OUTLIER) cc_final: 0.5386 (mt) REVERT: A 2006 MET cc_start: 0.4171 (tpt) cc_final: 0.2654 (ttt) REVERT: A 2289 MET cc_start: 0.0076 (tpt) cc_final: -0.1661 (ptm) outliers start: 55 outliers final: 36 residues processed: 180 average time/residue: 0.5110 time to fit residues: 106.3914 Evaluate side-chains 174 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 127 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 751 LYS Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1212 LYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1230 PHE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1264 TRP Chi-restraints excluded: chain A residue 1328 SER Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1390 ASN Chi-restraints excluded: chain A residue 1391 PHE Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1462 TYR Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1626 CYS Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 1988 THR Chi-restraints excluded: chain A residue 1992 THR Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2320 TYR Chi-restraints excluded: chain A residue 2345 THR Chi-restraints excluded: chain A residue 2361 VAL Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 121 optimal weight: 8.9990 chunk 186 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 116 optimal weight: 50.0000 chunk 177 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 225 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1724 ASN ** A2058 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.197161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.120526 restraints weight = 27223.391| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.80 r_work: 0.2995 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19413 Z= 0.161 Angle : 0.563 11.346 26261 Z= 0.301 Chirality : 0.046 0.175 2898 Planarity : 0.004 0.082 3394 Dihedral : 4.877 48.317 2562 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.51 % Favored : 95.45 % Rotamer: Outliers : 3.05 % Allowed : 24.74 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.47 (0.17), residues: 2351 helix: 2.22 (0.20), residues: 665 sheet: -0.05 (0.24), residues: 476 loop : -0.61 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1653 TYR 0.024 0.001 TYR A1459 PHE 0.035 0.001 PHE A1474 TRP 0.009 0.001 TRP A 118 HIS 0.004 0.001 HIS A1456 Details of bonding type rmsd covalent geometry : bond 0.00386 (19409) covalent geometry : angle 0.56286 (26261) hydrogen bonds : bond 0.05032 ( 830) hydrogen bonds : angle 4.56545 ( 2232) metal coordination : bond 0.00939 ( 3) Misc. bond : bond 0.00491 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10668.41 seconds wall clock time: 181 minutes 48.68 seconds (10908.68 seconds total)