Starting phenix.real_space_refine on Tue Jun 17 01:36:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jb5_36141/06_2025/8jb5_36141.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jb5_36141/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jb5_36141/06_2025/8jb5_36141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jb5_36141/06_2025/8jb5_36141.map" model { file = "/net/cci-nas-00/data/ceres_data/8jb5_36141/06_2025/8jb5_36141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jb5_36141/06_2025/8jb5_36141.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.60, per 1000 atoms: 0.56 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: 4.75 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 3.91 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: 13.98 Time building geometry restraints manager: 5.69 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 57.490 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:16.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.170 ------------------------------------------------------------------------------- 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 : 14.17 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.002 TRP A 102 HIS 0.005 0.001 HIS A 99 PHE 0.016 0.002 PHE A 503 TYR 0.019 0.002 TYR A1646 ARG 0.005 0.001 ARG A1241 Details of bonding type rmsd hydrogen bonds : bond 0.14813 ( 830) hydrogen bonds : angle 6.57421 ( 2232) metal coordination : bond 0.17488 ( 3) covalent geometry : bond 0.00751 (19409) covalent geometry : angle 0.88437 (26261) 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 : 2.172 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: 0.9998 time to fit residues: 372.2282 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 : 2.254 ------------------------------------------------------------------------------- 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 198 optimal weight: 7.9990 chunk 178 optimal weight: 0.1980 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 120 optimal weight: 20.0000 chunk 95 optimal weight: 0.9990 chunk 184 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 106 GLN A 380 ASN A 413 ASN A 574 ASN A 639 GLN A 732 GLN A 741 GLN A 876 ASN A 941 ASN A 949 ASN A 988 GLN A1109 ASN A1257 HIS A1584 ASN A1590 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.198865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122492 restraints weight = 27432.628| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.78 r_work: 0.3021 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19413 Z= 0.121 Angle : 0.559 9.687 26261 Z= 0.304 Chirality : 0.045 0.170 2898 Planarity : 0.004 0.092 3394 Dihedral : 7.230 68.177 2670 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.62 % Rotamer: Outliers : 3.76 % Allowed : 20.75 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.17), residues: 2351 helix: 1.56 (0.20), residues: 662 sheet: -0.60 (0.22), residues: 475 loop : -1.27 (0.16), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1949 HIS 0.005 0.001 HIS A 924 PHE 0.017 0.001 PHE A 937 TYR 0.016 0.001 TYR A 990 ARG 0.002 0.000 ARG A 526 Details of bonding type rmsd hydrogen bonds : bond 0.04707 ( 830) hydrogen bonds : angle 4.95570 ( 2232) metal coordination : bond 0.00905 ( 3) covalent geometry : bond 0.00258 (19409) covalent geometry : angle 0.55893 (26261) Misc. bond : bond 0.00673 ( 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 233 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 153 time to evaluate : 1.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8470 (tptp) REVERT: A 535 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8769 (mtmm) REVERT: A 646 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8714 (tp) REVERT: A 760 LYS cc_start: 0.8956 (mttt) cc_final: 0.8678 (mmtp) REVERT: A 1027 GLU cc_start: 0.7588 (tt0) cc_final: 0.7036 (tm-30) REVERT: A 1212 LYS cc_start: 0.0709 (OUTLIER) cc_final: 0.0478 (mmtm) REVERT: A 1230 PHE cc_start: 0.0178 (OUTLIER) cc_final: -0.0259 (m-80) REVERT: A 1302 VAL cc_start: 0.5444 (OUTLIER) cc_final: 0.4836 (p) REVERT: A 1332 MET cc_start: 0.4457 (pmm) cc_final: 0.0881 (ttp) REVERT: A 1462 TYR cc_start: 0.6727 (OUTLIER) cc_final: 0.3724 (p90) REVERT: A 1470 LYS cc_start: 0.7867 (ttmt) cc_final: 0.7511 (mtmt) REVERT: A 1477 TYR cc_start: 0.7620 (t80) cc_final: 0.6855 (t80) REVERT: A 1490 ASN cc_start: 0.7346 (p0) cc_final: 0.6997 (p0) REVERT: A 1499 MET cc_start: 0.6561 (tpp) cc_final: 0.5178 (ttp) REVERT: A 1567 LYS cc_start: 0.9089 (ttmt) cc_final: 0.8639 (ttpm) REVERT: A 1576 LEU cc_start: 0.2589 (OUTLIER) cc_final: 0.1956 (mp) REVERT: A 1775 ASP cc_start: 0.4947 (OUTLIER) cc_final: 0.3801 (m-30) REVERT: A 2006 MET cc_start: 0.4330 (tpt) cc_final: 0.2609 (ttt) outliers start: 80 outliers final: 33 residues processed: 226 average time/residue: 1.1171 time to fit residues: 292.3621 Evaluate side-chains 170 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 2.036 ------------------------------------------------------------------------------- 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 223 LYS 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 837 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 874 HIS 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 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 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 1814 PHE Chi-restraints excluded: chain A residue 1842 SER 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 139 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 161 optimal weight: 0.9980 chunk 198 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 795 HIS A1580 ASN A1633 GLN A1724 ASN A2058 ASN A2260 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.196240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.118992 restraints weight = 27061.210| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.82 r_work: 0.2968 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19413 Z= 0.166 Angle : 0.572 8.069 26261 Z= 0.311 Chirality : 0.047 0.175 2898 Planarity : 0.004 0.090 3394 Dihedral : 5.920 57.207 2579 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.08 % Allowed : 20.94 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2351 helix: 1.79 (0.20), residues: 663 sheet: -0.47 (0.23), residues: 465 loop : -1.03 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 118 HIS 0.005 0.001 HIS A 492 PHE 0.028 0.002 PHE A 937 TYR 0.014 0.001 TYR A1646 ARG 0.006 0.000 ARG A1495 Details of bonding type rmsd hydrogen bonds : bond 0.05554 ( 830) hydrogen bonds : angle 4.87502 ( 2232) metal coordination : bond 0.00947 ( 3) covalent geometry : bond 0.00391 (19409) covalent geometry : angle 0.57193 (26261) Misc. bond : bond 0.00576 ( 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 224 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 137 time to evaluate : 2.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8426 (t0) REVERT: A 227 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8228 (mt-10) REVERT: A 279 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7809 (mt-10) REVERT: A 333 LYS cc_start: 0.8743 (tmmt) cc_final: 0.8337 (mtmm) REVERT: A 543 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7865 (mt) REVERT: A 646 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.8830 (tp) REVERT: A 751 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8386 (mttm) REVERT: A 760 LYS cc_start: 0.9158 (mttt) cc_final: 0.8800 (mmtp) REVERT: A 1027 GLU cc_start: 0.7717 (tt0) cc_final: 0.7080 (tm-30) REVERT: A 1212 LYS cc_start: 0.0799 (OUTLIER) cc_final: 0.0506 (mmtm) REVERT: A 1230 PHE cc_start: 0.0163 (OUTLIER) cc_final: -0.0429 (m-80) REVERT: A 1302 VAL cc_start: 0.5707 (OUTLIER) cc_final: 0.5048 (p) REVERT: A 1327 LEU cc_start: 0.6492 (OUTLIER) cc_final: 0.6171 (OUTLIER) REVERT: A 1332 MET cc_start: 0.4407 (pmm) cc_final: 0.0811 (ttp) REVERT: A 1462 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.3753 (p90) REVERT: A 1470 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7651 (mtmt) REVERT: A 1477 TYR cc_start: 0.7557 (t80) cc_final: 0.6908 (t80) REVERT: A 1484 PHE cc_start: 0.8557 (m-80) cc_final: 0.8344 (m-80) REVERT: A 1490 ASN cc_start: 0.7355 (p0) cc_final: 0.7026 (p0) REVERT: A 1567 LYS cc_start: 0.9163 (ttmt) cc_final: 0.8700 (ttpm) REVERT: A 1775 ASP cc_start: 0.4912 (OUTLIER) cc_final: 0.3790 (m-30) REVERT: A 1788 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8886 (mttp) REVERT: A 2006 MET cc_start: 0.4393 (tpt) cc_final: 0.2657 (ttt) outliers start: 87 outliers final: 43 residues processed: 211 average time/residue: 1.3822 time to fit residues: 338.6586 Evaluate side-chains 176 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 123 time to evaluate : 2.559 ------------------------------------------------------------------------------- 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 381 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 543 LEU 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 837 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 873 LYS 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 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 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 1779 ASP Chi-restraints excluded: chain A residue 1788 LYS 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 2125 ILE Chi-restraints excluded: chain A residue 2235 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 93 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 123 optimal weight: 20.0000 chunk 222 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 183 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 A 574 ASN A1580 ASN A1584 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 = 0.4289 r_free = 0.4289 target = 0.196385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.119950 restraints weight = 27071.593| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.71 r_work: 0.3002 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19413 Z= 0.187 Angle : 0.580 9.059 26261 Z= 0.314 Chirality : 0.047 0.192 2898 Planarity : 0.004 0.091 3394 Dihedral : 5.705 57.868 2570 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.46 % Allowed : 21.64 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.17), residues: 2351 helix: 1.78 (0.20), residues: 664 sheet: -0.43 (0.23), residues: 465 loop : -0.97 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 118 HIS 0.004 0.001 HIS A1456 PHE 0.026 0.002 PHE A1474 TYR 0.017 0.002 TYR A 990 ARG 0.003 0.000 ARG A1495 Details of bonding type rmsd hydrogen bonds : bond 0.05634 ( 830) hydrogen bonds : angle 4.85800 ( 2232) metal coordination : bond 0.01108 ( 3) covalent geometry : bond 0.00450 (19409) covalent geometry : angle 0.58026 (26261) Misc. bond : bond 0.00549 ( 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 230 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 135 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7749 (mt-10) REVERT: A 333 LYS cc_start: 0.8692 (tmmt) cc_final: 0.8252 (mmtt) REVERT: A 543 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7833 (mt) REVERT: A 646 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.8784 (tp) REVERT: A 751 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8367 (mttm) REVERT: A 760 LYS cc_start: 0.9126 (mttt) cc_final: 0.8762 (mmtp) REVERT: A 814 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7593 (p0) REVERT: A 897 ARG cc_start: 0.6440 (OUTLIER) cc_final: 0.5749 (ptm160) REVERT: A 1027 GLU cc_start: 0.7700 (tt0) cc_final: 0.7279 (tm-30) REVERT: A 1029 LEU cc_start: 0.7573 (tp) cc_final: 0.7354 (tp) REVERT: A 1230 PHE cc_start: 0.0327 (OUTLIER) cc_final: -0.0381 (m-80) REVERT: A 1302 VAL cc_start: 0.5737 (OUTLIER) cc_final: 0.5101 (p) REVERT: A 1332 MET cc_start: 0.4529 (pmm) cc_final: 0.1019 (ttp) REVERT: A 1462 TYR cc_start: 0.7039 (OUTLIER) cc_final: 0.3841 (p90) REVERT: A 1470 LYS cc_start: 0.7987 (ttmt) cc_final: 0.7642 (mtmt) REVERT: A 1477 TYR cc_start: 0.7516 (t80) cc_final: 0.6858 (t80) REVERT: A 1490 ASN cc_start: 0.7367 (p0) cc_final: 0.7043 (p0) REVERT: A 1495 ARG cc_start: 0.8285 (ttm-80) cc_final: 0.7894 (mmm-85) REVERT: A 1499 MET cc_start: 0.6875 (tpp) cc_final: 0.5520 (ttp) REVERT: A 1567 LYS cc_start: 0.9133 (ttmt) cc_final: 0.8832 (tttm) REVERT: A 1576 LEU cc_start: 0.2826 (OUTLIER) cc_final: 0.2131 (mp) REVERT: A 1906 LEU cc_start: 0.7930 (mm) cc_final: 0.7619 (mp) REVERT: A 2006 MET cc_start: 0.4365 (tpt) cc_final: 0.2671 (ttt) outliers start: 95 outliers final: 50 residues processed: 217 average time/residue: 1.0516 time to fit residues: 267.5491 Evaluate side-chains 184 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 125 time to evaluate : 2.061 ------------------------------------------------------------------------------- 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 94 VAL Chi-restraints excluded: chain A residue 145 ILE 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 543 LEU 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 958 THR 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 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 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 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 1775 ASP 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 1895 LEU 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 1988 THR Chi-restraints excluded: chain A residue 2125 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 173 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 A1530 ASN A1580 ASN A1724 ASN A2058 ASN A2143 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.195985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.118991 restraints weight = 27475.639| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.67 r_work: 0.2957 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19413 Z= 0.158 Angle : 0.551 11.094 26261 Z= 0.297 Chirality : 0.046 0.212 2898 Planarity : 0.004 0.090 3394 Dihedral : 5.498 56.803 2569 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.32 % Allowed : 22.16 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.17), residues: 2351 helix: 1.94 (0.20), residues: 661 sheet: -0.40 (0.23), residues: 482 loop : -0.89 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 118 HIS 0.003 0.001 HIS A1456 PHE 0.030 0.001 PHE A1474 TYR 0.015 0.001 TYR A1646 ARG 0.003 0.000 ARG A1495 Details of bonding type rmsd hydrogen bonds : bond 0.05114 ( 830) hydrogen bonds : angle 4.74418 ( 2232) metal coordination : bond 0.00889 ( 3) covalent geometry : bond 0.00376 (19409) covalent geometry : angle 0.55056 (26261) Misc. bond : bond 0.00538 ( 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 228 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 136 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8332 (tpt) cc_final: 0.8013 (tpt) REVERT: A 238 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.7873 (m-40) REVERT: A 279 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7808 (mt-10) REVERT: A 333 LYS cc_start: 0.8680 (tmmt) cc_final: 0.8327 (mtmm) REVERT: A 543 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7786 (mt) REVERT: A 570 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.8366 (mmt) REVERT: A 646 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.8787 (tp) REVERT: A 751 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8373 (mttm) REVERT: A 814 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7600 (p0) REVERT: A 897 ARG cc_start: 0.6413 (OUTLIER) cc_final: 0.5678 (ptm160) REVERT: A 1027 GLU cc_start: 0.7719 (tt0) cc_final: 0.7404 (tm-30) REVERT: A 1029 LEU cc_start: 0.7564 (tp) cc_final: 0.7345 (tp) REVERT: A 1230 PHE cc_start: 0.0130 (OUTLIER) cc_final: -0.0452 (m-80) REVERT: A 1327 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6257 (tp) REVERT: A 1462 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.3939 (p90) REVERT: A 1470 LYS cc_start: 0.8001 (ttmt) cc_final: 0.7647 (mtmt) REVERT: A 1477 TYR cc_start: 0.7586 (t80) cc_final: 0.6920 (t80) REVERT: A 1490 ASN cc_start: 0.7434 (p0) cc_final: 0.7096 (p0) REVERT: A 1495 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7792 (mmm-85) REVERT: A 1499 MET cc_start: 0.6799 (tpp) cc_final: 0.5542 (ttp) REVERT: A 1567 LYS cc_start: 0.9182 (ttmt) cc_final: 0.8704 (ttpm) REVERT: A 1807 ASP cc_start: 0.8253 (t0) cc_final: 0.8023 (t0) REVERT: A 1906 LEU cc_start: 0.7954 (mm) cc_final: 0.7646 (mp) REVERT: A 1917 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6363 (tm-30) REVERT: A 2006 MET cc_start: 0.4266 (tpt) cc_final: 0.2645 (ttt) REVERT: A 2289 MET cc_start: -0.0592 (tpt) cc_final: -0.2462 (ptm) outliers start: 92 outliers final: 47 residues processed: 215 average time/residue: 1.0217 time to fit residues: 257.8683 Evaluate side-chains 181 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 123 time to evaluate : 2.273 ------------------------------------------------------------------------------- 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 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 543 LEU Chi-restraints excluded: chain A residue 570 MET 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 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 958 THR 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 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 1305 THR Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1328 SER 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 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 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 1988 THR Chi-restraints excluded: chain A residue 2125 ILE 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 133 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 102 optimal weight: 0.0970 chunk 146 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- 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 = 0.4301 r_free = 0.4301 target = 0.197344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.121322 restraints weight = 27341.334| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.99 r_work: 0.3019 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19413 Z= 0.117 Angle : 0.517 9.386 26261 Z= 0.279 Chirality : 0.045 0.208 2898 Planarity : 0.004 0.088 3394 Dihedral : 5.292 59.260 2569 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.99 % Allowed : 22.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2351 helix: 2.15 (0.21), residues: 665 sheet: -0.27 (0.23), residues: 489 loop : -0.78 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 118 HIS 0.003 0.001 HIS A 924 PHE 0.031 0.001 PHE A1474 TYR 0.019 0.001 TYR A 990 ARG 0.003 0.000 ARG A1495 Details of bonding type rmsd hydrogen bonds : bond 0.04426 ( 830) hydrogen bonds : angle 4.60208 ( 2232) metal coordination : bond 0.00548 ( 3) covalent geometry : bond 0.00264 (19409) covalent geometry : angle 0.51687 (26261) Misc. bond : bond 0.00550 ( 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 222 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 137 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8319 (tpt) cc_final: 0.8003 (tpt) REVERT: A 197 ASN cc_start: 0.7478 (m-40) cc_final: 0.6831 (t0) REVERT: A 279 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7631 (mt-10) REVERT: A 333 LYS cc_start: 0.8662 (tmmt) cc_final: 0.8305 (mtmm) REVERT: A 543 LEU cc_start: 0.8029 (mt) cc_final: 0.7715 (mt) REVERT: A 570 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8210 (mmt) REVERT: A 646 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8770 (tp) REVERT: A 814 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7411 (p0) REVERT: A 897 ARG cc_start: 0.6307 (OUTLIER) cc_final: 0.5613 (ptm160) REVERT: A 1029 LEU cc_start: 0.7585 (tp) cc_final: 0.7326 (tp) REVERT: A 1230 PHE cc_start: 0.0025 (OUTLIER) cc_final: -0.0497 (m-80) REVERT: A 1302 VAL cc_start: 0.5699 (OUTLIER) cc_final: 0.5158 (p) REVERT: A 1327 LEU cc_start: 0.6449 (OUTLIER) cc_final: 0.6147 (tp) REVERT: A 1332 MET cc_start: 0.4280 (pmm) cc_final: 0.0602 (ttp) REVERT: A 1391 PHE cc_start: 0.6529 (OUTLIER) cc_final: 0.5867 (p90) REVERT: A 1462 TYR cc_start: 0.7171 (OUTLIER) cc_final: 0.3929 (p90) REVERT: A 1470 LYS cc_start: 0.7979 (ttmt) cc_final: 0.7548 (mtmm) REVERT: A 1477 TYR cc_start: 0.7611 (t80) cc_final: 0.6968 (t80) REVERT: A 1490 ASN cc_start: 0.7309 (p0) cc_final: 0.6982 (p0) REVERT: A 1495 ARG cc_start: 0.8125 (ttm-80) cc_final: 0.7704 (mmm-85) REVERT: A 1499 MET cc_start: 0.6615 (tpp) cc_final: 0.5324 (ttp) REVERT: A 1567 LYS cc_start: 0.9141 (ttmt) cc_final: 0.8658 (ttpm) REVERT: A 1641 ILE cc_start: 0.8458 (mt) cc_final: 0.8202 (mt) REVERT: A 1906 LEU cc_start: 0.7899 (mm) cc_final: 0.7618 (mp) REVERT: A 2006 MET cc_start: 0.4260 (tpt) cc_final: 0.2552 (ttt) REVERT: A 2289 MET cc_start: -0.0479 (tpt) cc_final: -0.2394 (ptm) outliers start: 85 outliers final: 48 residues processed: 211 average time/residue: 1.0653 time to fit residues: 264.1465 Evaluate side-chains 186 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 129 time to evaluate : 2.167 ------------------------------------------------------------------------------- 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 395 CYS Chi-restraints excluded: chain A residue 414 LEU 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 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 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 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 1064 ILE Chi-restraints excluded: chain A residue 1072 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 1302 VAL 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 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 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 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 2125 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 58 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 232 optimal weight: 0.0030 chunk 163 optimal weight: 3.9990 chunk 41 optimal weight: 0.3980 chunk 160 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- 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 A1445 GLN A1580 ASN A1724 ASN A2058 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.197968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.119584 restraints weight = 27075.815| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.55 r_work: 0.3013 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2623 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= 0.119 Angle : 0.519 8.235 26261 Z= 0.281 Chirality : 0.045 0.213 2898 Planarity : 0.004 0.086 3394 Dihedral : 5.109 56.383 2568 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.71 % Allowed : 23.29 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.17), residues: 2351 helix: 2.21 (0.20), residues: 665 sheet: -0.16 (0.23), residues: 485 loop : -0.72 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 118 HIS 0.003 0.001 HIS A 924 PHE 0.032 0.001 PHE A1474 TYR 0.013 0.001 TYR A1646 ARG 0.003 0.000 ARG A1495 Details of bonding type rmsd hydrogen bonds : bond 0.04360 ( 830) hydrogen bonds : angle 4.53438 ( 2232) metal coordination : bond 0.00578 ( 3) covalent geometry : bond 0.00271 (19409) covalent geometry : angle 0.51871 (26261) Misc. bond : bond 0.00515 ( 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: 79 poor density : 135 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8325 (tpt) cc_final: 0.8005 (tpt) REVERT: A 197 ASN cc_start: 0.7452 (m-40) cc_final: 0.6855 (t0) REVERT: A 238 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.7910 (m-40) REVERT: A 333 LYS cc_start: 0.8671 (tmmt) cc_final: 0.8322 (mtmm) REVERT: A 543 LEU cc_start: 0.7991 (mt) cc_final: 0.7679 (mt) REVERT: A 570 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8212 (mmt) REVERT: A 646 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.8804 (tp) REVERT: A 814 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7434 (p0) REVERT: A 1029 LEU cc_start: 0.7703 (tp) cc_final: 0.7452 (tp) REVERT: A 1212 LYS cc_start: 0.1211 (OUTLIER) cc_final: 0.0948 (mmtm) REVERT: A 1230 PHE cc_start: 0.0119 (OUTLIER) cc_final: -0.0497 (m-80) REVERT: A 1327 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6236 (tp) REVERT: A 1332 MET cc_start: 0.4384 (pmm) cc_final: 0.0789 (ttp) REVERT: A 1391 PHE cc_start: 0.6581 (OUTLIER) cc_final: 0.5896 (p90) REVERT: A 1462 TYR cc_start: 0.7202 (OUTLIER) cc_final: 0.3867 (p90) REVERT: A 1470 LYS cc_start: 0.7984 (ttmt) cc_final: 0.7569 (mtmm) REVERT: A 1477 TYR cc_start: 0.7619 (t80) cc_final: 0.7000 (t80) REVERT: A 1490 ASN cc_start: 0.7314 (p0) cc_final: 0.7005 (p0) REVERT: A 1495 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7946 (mmm-85) REVERT: A 1496 ASN cc_start: 0.7047 (t0) cc_final: 0.6477 (m-40) REVERT: A 1499 MET cc_start: 0.6488 (tpp) cc_final: 0.5175 (ttp) REVERT: A 1567 LYS cc_start: 0.9165 (ttmt) cc_final: 0.8713 (ttpm) REVERT: A 1641 ILE cc_start: 0.8511 (mt) cc_final: 0.8246 (mt) REVERT: A 1906 LEU cc_start: 0.7928 (mm) cc_final: 0.7673 (mp) REVERT: A 2006 MET cc_start: 0.4091 (tpt) cc_final: 0.2720 (ttt) REVERT: A 2289 MET cc_start: -0.0217 (tpt) cc_final: -0.2174 (ptm) outliers start: 79 outliers final: 49 residues processed: 201 average time/residue: 0.9944 time to fit residues: 235.7173 Evaluate side-chains 182 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 124 time to evaluate : 2.004 ------------------------------------------------------------------------------- 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 395 CYS Chi-restraints excluded: chain A residue 414 LEU 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 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 874 HIS 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 958 THR Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1025 LEU 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 108 optimal weight: 0.0270 chunk 160 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 chunk 37 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 overall best weight: 1.2244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** A1590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4301 r_free = 0.4301 target = 0.197538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.122011 restraints weight = 27391.140| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.91 r_work: 0.3006 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19413 Z= 0.128 Angle : 0.532 12.387 26261 Z= 0.288 Chirality : 0.046 0.221 2898 Planarity : 0.004 0.084 3394 Dihedral : 5.029 54.044 2567 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.42 % Favored : 95.53 % Rotamer: Outliers : 3.43 % Allowed : 23.80 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2351 helix: 2.24 (0.20), residues: 665 sheet: -0.13 (0.23), residues: 483 loop : -0.69 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 118 HIS 0.003 0.001 HIS A 924 PHE 0.033 0.001 PHE A1474 TYR 0.020 0.001 TYR A 990 ARG 0.003 0.000 ARG A1495 Details of bonding type rmsd hydrogen bonds : bond 0.04498 ( 830) hydrogen bonds : angle 4.52729 ( 2232) metal coordination : bond 0.00689 ( 3) covalent geometry : bond 0.00296 (19409) covalent geometry : angle 0.53172 (26261) Misc. bond : bond 0.00506 ( 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 202 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 129 time to evaluate : 2.276 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: 0.8312 (tpt) cc_final: 0.7992 (tpt) REVERT: A 197 ASN cc_start: 0.7440 (m-40) cc_final: 0.6879 (t0) REVERT: A 333 LYS cc_start: 0.8666 (tmmt) cc_final: 0.8328 (mtmm) REVERT: A 543 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7678 (mt) REVERT: A 570 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8190 (mmt) REVERT: A 646 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8753 (tp) REVERT: A 751 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8348 (mttm) REVERT: A 814 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7425 (p0) REVERT: A 1029 LEU cc_start: 0.7585 (tp) cc_final: 0.7300 (tp) REVERT: A 1212 LYS cc_start: 0.1226 (OUTLIER) cc_final: 0.0954 (mmtm) REVERT: A 1230 PHE cc_start: 0.0255 (OUTLIER) cc_final: -0.0429 (m-80) REVERT: A 1327 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6229 (tp) REVERT: A 1332 MET cc_start: 0.4390 (pmm) cc_final: 0.0795 (ttp) REVERT: A 1391 PHE cc_start: 0.6559 (OUTLIER) cc_final: 0.5886 (p90) REVERT: A 1470 LYS cc_start: 0.7989 (ttmt) cc_final: 0.7570 (mtmm) REVERT: A 1477 TYR cc_start: 0.7617 (t80) cc_final: 0.7011 (t80) REVERT: A 1490 ASN cc_start: 0.7223 (p0) cc_final: 0.6933 (p0) REVERT: A 1495 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7863 (mmm-85) REVERT: A 1496 ASN cc_start: 0.7096 (t0) cc_final: 0.6555 (m-40) REVERT: A 1499 MET cc_start: 0.6503 (tpp) cc_final: 0.5171 (ttp) REVERT: A 1567 LYS cc_start: 0.9167 (ttmt) cc_final: 0.8715 (ttpm) REVERT: A 1641 ILE cc_start: 0.8477 (mt) cc_final: 0.8209 (mt) REVERT: A 1906 LEU cc_start: 0.7781 (mm) cc_final: 0.7528 (mp) REVERT: A 2006 MET cc_start: 0.4064 (tpt) cc_final: 0.2688 (ttt) REVERT: A 2289 MET cc_start: -0.0293 (tpt) cc_final: -0.2312 (ptm) outliers start: 73 outliers final: 50 residues processed: 191 average time/residue: 1.0373 time to fit residues: 236.2815 Evaluate side-chains 180 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 121 time to evaluate : 2.009 ------------------------------------------------------------------------------- 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 395 CYS Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 543 LEU 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 874 HIS 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 958 THR Chi-restraints excluded: chain A residue 1025 LEU 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 17 optimal weight: 0.6980 chunk 226 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 132 optimal weight: 0.0370 chunk 114 optimal weight: 30.0000 chunk 197 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 overall best weight: 1.9462 ------------------------------------------------------------------------------- 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 A1724 ASN ** A2058 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.196076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.119612 restraints weight = 27238.290| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.82 r_work: 0.2982 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19413 Z= 0.170 Angle : 0.561 11.869 26261 Z= 0.304 Chirality : 0.047 0.234 2898 Planarity : 0.004 0.083 3394 Dihedral : 5.153 53.531 2565 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.68 % Favored : 95.28 % Rotamer: Outliers : 3.29 % Allowed : 23.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2351 helix: 2.08 (0.20), residues: 665 sheet: -0.17 (0.23), residues: 476 loop : -0.75 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 118 HIS 0.004 0.001 HIS A1456 PHE 0.034 0.001 PHE A1474 TYR 0.018 0.001 TYR A 990 ARG 0.002 0.000 ARG A1495 Details of bonding type rmsd hydrogen bonds : bond 0.05301 ( 830) hydrogen bonds : angle 4.67020 ( 2232) metal coordination : bond 0.00974 ( 3) covalent geometry : bond 0.00406 (19409) covalent geometry : angle 0.56131 (26261) Misc. bond : bond 0.00497 ( 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 199 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 129 time to evaluate : 2.128 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: 0.8310 (tpt) cc_final: 0.7990 (tpt) REVERT: A 197 ASN cc_start: 0.7686 (m-40) cc_final: 0.7008 (t0) REVERT: A 238 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.7847 (m-40) REVERT: A 333 LYS cc_start: 0.8667 (tmmt) cc_final: 0.8325 (mtmm) REVERT: A 543 LEU cc_start: 0.8140 (mt) cc_final: 0.7751 (mt) REVERT: A 570 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8306 (mmt) REVERT: A 646 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.8763 (tp) REVERT: A 751 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8399 (mttm) REVERT: A 814 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7555 (p0) REVERT: A 1212 LYS cc_start: 0.1251 (OUTLIER) cc_final: 0.0987 (mmtm) REVERT: A 1230 PHE cc_start: 0.0265 (OUTLIER) cc_final: -0.0452 (m-80) REVERT: A 1302 VAL cc_start: 0.5899 (OUTLIER) cc_final: 0.5348 (p) REVERT: A 1327 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.6145 (tp) REVERT: A 1391 PHE cc_start: 0.6470 (OUTLIER) cc_final: 0.5772 (p90) REVERT: A 1470 LYS cc_start: 0.7990 (ttmt) cc_final: 0.7558 (mtmm) REVERT: A 1477 TYR cc_start: 0.7603 (t80) cc_final: 0.6988 (t80) REVERT: A 1490 ASN cc_start: 0.7206 (p0) cc_final: 0.6926 (p0) REVERT: A 1495 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7821 (mmm-85) REVERT: A 1496 ASN cc_start: 0.7089 (t0) cc_final: 0.6741 (m-40) REVERT: A 1499 MET cc_start: 0.6554 (tpp) cc_final: 0.5224 (ttp) REVERT: A 1567 LYS cc_start: 0.9161 (ttmt) cc_final: 0.8690 (ttpm) REVERT: A 1641 ILE cc_start: 0.8501 (mt) cc_final: 0.8258 (mt) REVERT: A 1906 LEU cc_start: 0.7822 (mm) cc_final: 0.7589 (mp) REVERT: A 2006 MET cc_start: 0.4103 (tpt) cc_final: 0.2854 (ttt) REVERT: A 2289 MET cc_start: -0.0289 (tpt) cc_final: -0.2348 (ptm) outliers start: 70 outliers final: 50 residues processed: 191 average time/residue: 0.9722 time to fit residues: 220.1692 Evaluate side-chains 188 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 128 time to evaluate : 2.086 ------------------------------------------------------------------------------- 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 94 VAL Chi-restraints excluded: chain A residue 145 ILE 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 395 CYS Chi-restraints excluded: chain A residue 414 LEU 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 884 ILE Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 968 LEU 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 1302 VAL 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 1391 PHE Chi-restraints excluded: chain A residue 1418 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 153 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 160 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.197239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.121644 restraints weight = 27256.361| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.76 r_work: 0.3011 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19413 Z= 0.121 Angle : 0.530 11.761 26261 Z= 0.286 Chirality : 0.046 0.235 2898 Planarity : 0.004 0.084 3394 Dihedral : 4.914 50.591 2563 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.55 % Favored : 95.41 % Rotamer: Outliers : 2.77 % Allowed : 24.74 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.17), residues: 2351 helix: 2.22 (0.20), residues: 666 sheet: -0.08 (0.23), residues: 482 loop : -0.69 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 118 HIS 0.003 0.001 HIS A 924 PHE 0.033 0.001 PHE A1474 TYR 0.019 0.001 TYR A 990 ARG 0.003 0.000 ARG A 241 Details of bonding type rmsd hydrogen bonds : bond 0.04485 ( 830) hydrogen bonds : angle 4.55542 ( 2232) metal coordination : bond 0.00568 ( 3) covalent geometry : bond 0.00271 (19409) covalent geometry : angle 0.53046 (26261) Misc. bond : bond 0.00485 ( 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: 59 poor density : 128 time to evaluate : 2.069 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: 0.8311 (tpt) cc_final: 0.7992 (tpt) REVERT: A 197 ASN cc_start: 0.7514 (m-40) cc_final: 0.6930 (t0) REVERT: A 333 LYS cc_start: 0.8656 (tmmt) cc_final: 0.8319 (mtmm) REVERT: A 543 LEU cc_start: 0.7986 (mt) cc_final: 0.7608 (mt) REVERT: A 570 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8200 (mmt) REVERT: A 646 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.8739 (tp) REVERT: A 751 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8350 (mttm) REVERT: A 814 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7442 (p0) REVERT: A 1212 LYS cc_start: 0.1231 (OUTLIER) cc_final: 0.0972 (mmtm) REVERT: A 1230 PHE cc_start: 0.0224 (OUTLIER) cc_final: -0.0449 (m-80) REVERT: A 1327 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6221 (tp) REVERT: A 1332 MET cc_start: 0.4392 (pmm) cc_final: 0.0864 (tpp) REVERT: A 1391 PHE cc_start: 0.6554 (OUTLIER) cc_final: 0.5871 (p90) REVERT: A 1470 LYS cc_start: 0.7958 (ttmt) cc_final: 0.7535 (mtmm) REVERT: A 1477 TYR cc_start: 0.7599 (t80) cc_final: 0.6987 (t80) REVERT: A 1490 ASN cc_start: 0.7216 (p0) cc_final: 0.6933 (p0) REVERT: A 1495 ARG cc_start: 0.8129 (ttm-80) cc_final: 0.7826 (mmm-85) REVERT: A 1496 ASN cc_start: 0.7078 (t0) cc_final: 0.6536 (m-40) REVERT: A 1499 MET cc_start: 0.6510 (tpp) cc_final: 0.5165 (ttp) REVERT: A 1567 LYS cc_start: 0.9161 (ttmt) cc_final: 0.8696 (ttpm) REVERT: A 1641 ILE cc_start: 0.8479 (mt) cc_final: 0.8210 (mt) REVERT: A 1906 LEU cc_start: 0.7827 (mm) cc_final: 0.7603 (mp) REVERT: A 1927 ILE cc_start: 0.6295 (OUTLIER) cc_final: 0.5956 (pp) REVERT: A 2006 MET cc_start: 0.3894 (tpt) cc_final: 0.2666 (ttt) REVERT: A 2289 MET cc_start: -0.0290 (tpt) cc_final: -0.2308 (ptm) outliers start: 59 outliers final: 43 residues processed: 181 average time/residue: 1.0416 time to fit residues: 222.0053 Evaluate side-chains 175 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 123 time to evaluate : 1.968 ------------------------------------------------------------------------------- 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 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 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 1064 ILE 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 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 1391 PHE Chi-restraints excluded: chain A residue 1418 ILE 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 2226 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 67 optimal weight: 0.7980 chunk 191 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 208 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 103 optimal weight: 0.0000 chunk 54 optimal weight: 0.0670 chunk 233 optimal weight: 40.0000 chunk 73 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 overall best weight: 0.5322 ------------------------------------------------------------------------------- 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 A1724 ASN A1931 ASN A2001 ASN ** A2058 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.199879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.119163 restraints weight = 27280.240| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.10 r_work: 0.3068 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19413 Z= 0.098 Angle : 0.498 11.767 26261 Z= 0.269 Chirality : 0.045 0.213 2898 Planarity : 0.003 0.085 3394 Dihedral : 4.607 48.685 2563 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 2.30 % Allowed : 25.21 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2351 helix: 2.43 (0.21), residues: 667 sheet: 0.04 (0.24), residues: 484 loop : -0.61 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 118 HIS 0.003 0.001 HIS A 924 PHE 0.032 0.001 PHE A1474 TYR 0.020 0.001 TYR A 990 ARG 0.002 0.000 ARG A1495 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 830) hydrogen bonds : angle 4.35354 ( 2232) metal coordination : bond 0.00369 ( 3) covalent geometry : bond 0.00208 (19409) covalent geometry : angle 0.49830 (26261) Misc. bond : bond 0.00480 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23500.22 seconds wall clock time: 403 minutes 42.17 seconds (24222.17 seconds total)