Starting phenix.real_space_refine on Sat Feb 7 13:44:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u1x_20614/02_2026/6u1x_20614.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u1x_20614/02_2026/6u1x_20614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6u1x_20614/02_2026/6u1x_20614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u1x_20614/02_2026/6u1x_20614.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u1x_20614/02_2026/6u1x_20614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u1x_20614/02_2026/6u1x_20614.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 0.033 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 92 5.16 5 C 10694 2.51 5 N 2907 2.21 5 O 3066 1.98 5 H 16768 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33529 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 33096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2059, 33096 Classifications: {'peptide': 2059} Link IDs: {'PTRANS': 97, 'TRANS': 1961} Chain breaks: 3 Chain: "P" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 431 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17047 SG CYS A1081 67.106 70.840 82.524 1.00 67.09 S ATOM 20315 SG CYS A1299 67.893 67.213 81.956 1.00 71.67 S ATOM 20358 SG CYS A1302 65.606 68.756 79.521 1.00 71.70 S ATOM 17656 SG CYS A1120 66.119 51.227 72.920 1.00 74.28 S ATOM 17690 SG CYS A1123 62.607 50.900 73.847 1.00 75.85 S Time building chain proxies: 6.19, per 1000 atoms: 0.18 Number of scatterers: 33529 At special positions: 0 Unit cell: (124.16, 132.89, 100.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 92 16.00 O 3066 8.00 N 2907 7.00 C 10694 6.00 H 16768 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3000 " pdb="ZN ZN A3000 " - pdb=" SG CYS A1299 " pdb="ZN ZN A3000 " - pdb=" SG CYS A1081 " pdb="ZN ZN A3000 " - pdb=" SG CYS A1302 " pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A1294 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A1296 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1123 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1120 " Number of angles added : 2 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3922 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 12 sheets defined 52.7% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 49 through 58 removed outlier: 3.522A pdb=" N LEU A 53 " --> pdb=" O ASP A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.572A pdb=" N ASP A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 68 " --> pdb=" O SER A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 68' Processing helix chain 'A' and resid 71 through 80 Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.683A pdb=" N SER A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 135 removed outlier: 3.598A pdb=" N ILE A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL A 126 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 146 Processing helix chain 'A' and resid 147 through 172 removed outlier: 4.247A pdb=" N ILE A 153 " --> pdb=" O ASP A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 186 Processing helix chain 'A' and resid 227 through 247 removed outlier: 3.526A pdb=" N LEU A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 278 removed outlier: 3.556A pdb=" N ILE A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 288 through 302 removed outlier: 3.542A pdb=" N ILE A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 327 removed outlier: 4.401A pdb=" N GLU A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 340 removed outlier: 3.698A pdb=" N PHE A 334 " --> pdb=" O ARG A 330 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET A 340 " --> pdb=" O HIS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 353 removed outlier: 3.883A pdb=" N THR A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 377 Processing helix chain 'A' and resid 383 through 407 removed outlier: 3.749A pdb=" N ALA A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 428 Processing helix chain 'A' and resid 433 through 438 removed outlier: 3.613A pdb=" N GLN A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 443 through 447 removed outlier: 3.562A pdb=" N LEU A 447 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 484 Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 505 through 517 Processing helix chain 'A' and resid 545 through 563 Processing helix chain 'A' and resid 564 through 567 Processing helix chain 'A' and resid 575 through 587 Processing helix chain 'A' and resid 614 through 629 Proline residue: A 620 - end of helix removed outlier: 3.714A pdb=" N MET A 625 " --> pdb=" O VAL A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 643 Processing helix chain 'A' and resid 684 through 704 Processing helix chain 'A' and resid 729 through 759 removed outlier: 3.636A pdb=" N LEU A 733 " --> pdb=" O ASN A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 795 removed outlier: 3.968A pdb=" N ARG A 793 " --> pdb=" O LEU A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 825 removed outlier: 3.687A pdb=" N SER A 813 " --> pdb=" O ALA A 809 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 814 " --> pdb=" O ASN A 810 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL A 815 " --> pdb=" O ILE A 811 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN A 818 " --> pdb=" O SER A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 850 removed outlier: 3.745A pdb=" N HIS A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 880 removed outlier: 3.985A pdb=" N LEU A 878 " --> pdb=" O LYS A 874 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 896 removed outlier: 3.540A pdb=" N ARG A 894 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 918 removed outlier: 3.548A pdb=" N LEU A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 931 removed outlier: 3.616A pdb=" N LYS A 924 " --> pdb=" O SER A 920 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET A 926 " --> pdb=" O HIS A 922 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A 929 " --> pdb=" O GLU A 925 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A 931 " --> pdb=" O SER A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 949 removed outlier: 3.507A pdb=" N LEU A 946 " --> pdb=" O HIS A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 976 Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 996 through 1006 removed outlier: 3.612A pdb=" N SER A1001 " --> pdb=" O ASP A 997 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A1006 " --> pdb=" O PHE A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1020 Processing helix chain 'A' and resid 1023 through 1031 removed outlier: 3.810A pdb=" N LEU A1029 " --> pdb=" O VAL A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1043 Processing helix chain 'A' and resid 1045 through 1069 removed outlier: 4.106A pdb=" N ARG A1049 " --> pdb=" O LYS A1045 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A1050 " --> pdb=" O LYS A1046 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A1051 " --> pdb=" O TYR A1047 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A1052 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASP A1053 " --> pdb=" O ARG A1049 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU A1054 " --> pdb=" O GLU A1050 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU A1059 " --> pdb=" O ILE A1055 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS A1065 " --> pdb=" O SER A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1095 Processing helix chain 'A' and resid 1105 through 1110 Processing helix chain 'A' and resid 1121 through 1126 removed outlier: 4.080A pdb=" N THR A1125 " --> pdb=" O ALA A1121 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1121 through 1126' Processing helix chain 'A' and resid 1174 through 1181 Processing helix chain 'A' and resid 1182 through 1186 Processing helix chain 'A' and resid 1196 through 1208 removed outlier: 3.617A pdb=" N ILE A1204 " --> pdb=" O ILE A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1248 removed outlier: 4.187A pdb=" N LEU A1247 " --> pdb=" O SER A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1263 removed outlier: 3.835A pdb=" N ASP A1262 " --> pdb=" O ASP A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1284 removed outlier: 3.535A pdb=" N THR A1272 " --> pdb=" O LEU A1268 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1377 Processing helix chain 'A' and resid 1379 through 1383 Processing helix chain 'A' and resid 1388 through 1392 removed outlier: 3.829A pdb=" N ILE A1391 " --> pdb=" O PRO A1388 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A1392 " --> pdb=" O LEU A1389 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1388 through 1392' Processing helix chain 'A' and resid 1396 through 1417 removed outlier: 3.529A pdb=" N PHE A1400 " --> pdb=" O ARG A1396 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE A1417 " --> pdb=" O CYS A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1427 through 1444 removed outlier: 3.737A pdb=" N ALA A1431 " --> pdb=" O ARG A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1451 Processing helix chain 'A' and resid 1456 through 1463 Processing helix chain 'A' and resid 1476 through 1493 removed outlier: 3.633A pdb=" N ILE A1483 " --> pdb=" O ASP A1479 " (cutoff:3.500A) Processing helix chain 'A' and resid 1510 through 1514 Processing helix chain 'A' and resid 1515 through 1534 Proline residue: A1521 - end of helix removed outlier: 4.568A pdb=" N THR A1526 " --> pdb=" O PHE A1522 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N THR A1527 " --> pdb=" O SER A1523 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A1528 " --> pdb=" O ILE A1524 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN A1530 " --> pdb=" O THR A1526 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS A1534 " --> pdb=" O GLN A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1538 through 1557 Processing helix chain 'A' and resid 1564 through 1568 removed outlier: 4.004A pdb=" N LYS A1567 " --> pdb=" O ILE A1564 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1583 removed outlier: 3.520A pdb=" N HIS A1582 " --> pdb=" O GLU A1579 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A1583 " --> pdb=" O ILE A1580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1579 through 1583' Processing helix chain 'A' and resid 1634 through 1640 Processing helix chain 'A' and resid 1648 through 1659 Processing helix chain 'A' and resid 1674 through 1684 Processing helix chain 'A' and resid 1710 through 1716 removed outlier: 3.529A pdb=" N LEU A1713 " --> pdb=" O PRO A1710 " (cutoff:3.500A) Processing helix chain 'A' and resid 1719 through 1723 removed outlier: 3.636A pdb=" N ARG A1722 " --> pdb=" O ASP A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1738 through 1753 removed outlier: 4.076A pdb=" N TRP A1742 " --> pdb=" O ASP A1738 " (cutoff:3.500A) Processing helix chain 'A' and resid 1767 through 1780 removed outlier: 3.535A pdb=" N SER A1771 " --> pdb=" O ASP A1767 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A1780 " --> pdb=" O THR A1776 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1786 Processing helix chain 'A' and resid 1798 through 1804 Processing helix chain 'A' and resid 1807 through 1815 Proline residue: A1814 - end of helix Processing helix chain 'A' and resid 1851 through 1854 Processing helix chain 'A' and resid 1855 through 1860 removed outlier: 4.322A pdb=" N LYS A1860 " --> pdb=" O ASN A1856 " (cutoff:3.500A) Processing helix chain 'A' and resid 1867 through 1880 removed outlier: 3.503A pdb=" N GLU A1871 " --> pdb=" O SER A1867 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A1874 " --> pdb=" O GLN A1870 " (cutoff:3.500A) Processing helix chain 'A' and resid 1888 through 1892 removed outlier: 3.547A pdb=" N PHE A1891 " --> pdb=" O PRO A1888 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A1892 " --> pdb=" O SER A1889 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1888 through 1892' Processing helix chain 'A' and resid 1894 through 1906 removed outlier: 3.514A pdb=" N GLU A1900 " --> pdb=" O PHE A1896 " (cutoff:3.500A) Processing helix chain 'A' and resid 1909 through 1923 removed outlier: 3.619A pdb=" N SER A1920 " --> pdb=" O ALA A1916 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A1921 " --> pdb=" O ALA A1917 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A1923 " --> pdb=" O LYS A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1927 through 1943 Processing helix chain 'A' and resid 1961 through 1980 removed outlier: 3.744A pdb=" N TRP A1974 " --> pdb=" O GLY A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1981 through 1994 Processing helix chain 'A' and resid 2029 through 2045 removed outlier: 3.769A pdb=" N ILE A2033 " --> pdb=" O SER A2029 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE A2037 " --> pdb=" O ILE A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2053 through 2063 removed outlier: 3.688A pdb=" N THR A2063 " --> pdb=" O GLN A2059 " (cutoff:3.500A) Processing helix chain 'A' and resid 2071 through 2076 removed outlier: 3.836A pdb=" N ARG A2075 " --> pdb=" O SER A2071 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A2076 " --> pdb=" O ASN A2072 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2071 through 2076' Processing helix chain 'A' and resid 2078 through 2084 Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 192 Processing sheet with id=AA2, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AA3, first strand: chain 'A' and resid 524 through 525 Processing sheet with id=AA4, first strand: chain 'A' and resid 707 through 711 removed outlier: 4.411A pdb=" N GLN A 716 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 770 " --> pdb=" O ALA A 601 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 707 through 711 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 Processing sheet with id=AA7, first strand: chain 'A' and resid 773 through 775 Processing sheet with id=AA8, first strand: chain 'A' and resid 1114 through 1115 removed outlier: 3.726A pdb=" N SER A1132 " --> pdb=" O THR A1253 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1151 through 1155 removed outlier: 5.333A pdb=" N TYR A1152 " --> pdb=" O TRP A2107 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ASP A2109 " --> pdb=" O TYR A1152 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY A1154 " --> pdb=" O ASP A2109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 1346 through 1347 removed outlier: 6.973A pdb=" N LEU A1346 " --> pdb=" O LEU A1575 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1609 through 1613 removed outlier: 7.033A pdb=" N GLY A1840 " --> pdb=" O LYS A1817 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL A1819 " --> pdb=" O CYS A1838 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N CYS A1838 " --> pdb=" O VAL A1819 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU A1821 " --> pdb=" O MET A1836 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N MET A1836 " --> pdb=" O LEU A1821 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLN A1823 " --> pdb=" O VAL A1834 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N VAL A1834 " --> pdb=" O GLN A1823 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU A1667 " --> pdb=" O VAL A1760 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2010 through 2014 733 hydrogen bonds defined for protein. 2106 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: 8.96 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16739 1.03 - 1.23: 29 1.23 - 1.42: 7198 1.42 - 1.62: 9807 1.62 - 1.81: 150 Bond restraints: 33923 Sorted by residual: bond pdb=" C ASN A1633 " pdb=" N PRO A1634 " ideal model delta sigma weight residual 1.331 1.346 -0.015 7.90e-03 1.60e+04 3.38e+00 bond pdb=" C LEU A1644 " pdb=" N PRO A1645 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.03e+00 bond pdb=" C LYS A1534 " pdb=" N PRO A1535 " ideal model delta sigma weight residual 1.335 1.349 -0.013 1.30e-02 5.92e+03 1.07e+00 bond pdb=" CG PRO A1106 " pdb=" CD PRO A1106 " ideal model delta sigma weight residual 1.503 1.470 0.033 3.40e-02 8.65e+02 9.69e-01 bond pdb=" CB PRO A1645 " pdb=" CG PRO A1645 " ideal model delta sigma weight residual 1.492 1.448 0.044 5.00e-02 4.00e+02 7.72e-01 ... (remaining 33918 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 57236 1.09 - 2.19: 3779 2.19 - 3.28: 215 3.28 - 4.37: 77 4.37 - 5.47: 28 Bond angle restraints: 61335 Sorted by residual: angle pdb=" N TYR A1473 " pdb=" CA TYR A1473 " pdb=" C TYR A1473 " ideal model delta sigma weight residual 109.41 104.09 5.32 1.53e+00 4.27e-01 1.21e+01 angle pdb=" N LEU A1644 " pdb=" CA LEU A1644 " pdb=" C LEU A1644 " ideal model delta sigma weight residual 109.87 104.87 5.00 1.62e+00 3.81e-01 9.53e+00 angle pdb=" C GLY A1753 " pdb=" N LEU A1754 " pdb=" CA LEU A1754 " ideal model delta sigma weight residual 121.54 126.94 -5.40 1.91e+00 2.74e-01 8.00e+00 angle pdb=" CA TYR A1473 " pdb=" C TYR A1473 " pdb=" N PRO A1474 " ideal model delta sigma weight residual 117.69 120.32 -2.63 9.30e-01 1.16e+00 7.99e+00 angle pdb=" N GLY A2007 " pdb=" CA GLY A2007 " pdb=" C GLY A2007 " ideal model delta sigma weight residual 113.18 108.13 5.05 2.37e+00 1.78e-01 4.55e+00 ... (remaining 61330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 14604 16.91 - 33.81: 1005 33.81 - 50.72: 218 50.72 - 67.62: 103 67.62 - 84.53: 5 Dihedral angle restraints: 15935 sinusoidal: 8694 harmonic: 7241 Sorted by residual: dihedral pdb=" CA TYR A1473 " pdb=" C TYR A1473 " pdb=" N PRO A1474 " pdb=" CA PRO A1474 " ideal model delta harmonic sigma weight residual -180.00 -132.20 -47.80 0 5.00e+00 4.00e-02 9.14e+01 dihedral pdb=" CA GLN A1643 " pdb=" C GLN A1643 " pdb=" N LEU A1644 " pdb=" CA LEU A1644 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PRO A1474 " pdb=" C PRO A1474 " pdb=" N THR A1475 " pdb=" CA THR A1475 " ideal model delta harmonic sigma weight residual -180.00 -156.94 -23.06 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 15932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1486 0.028 - 0.056: 749 0.056 - 0.084: 191 0.084 - 0.111: 92 0.111 - 0.139: 43 Chirality restraints: 2561 Sorted by residual: chirality pdb=" CA ILE A1469 " pdb=" N ILE A1469 " pdb=" C ILE A1469 " pdb=" CB ILE A1469 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CA ILE A1465 " pdb=" N ILE A1465 " pdb=" C ILE A1465 " pdb=" CB ILE A1465 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE A 455 " pdb=" N ILE A 455 " pdb=" C ILE A 455 " pdb=" CB ILE A 455 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 2558 not shown) Planarity restraints: 4933 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A1473 " -0.063 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO A1474 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO A1474 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A1474 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1060 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.78e+00 pdb=" C VAL A1060 " 0.038 2.00e-02 2.50e+03 pdb=" O VAL A1060 " -0.014 2.00e-02 2.50e+03 pdb=" N SER A1061 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A1058 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C SER A1058 " -0.028 2.00e-02 2.50e+03 pdb=" O SER A1058 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU A1059 " 0.009 2.00e-02 2.50e+03 ... (remaining 4930 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 4119 2.26 - 2.84: 76858 2.84 - 3.43: 84709 3.43 - 4.01: 119679 4.01 - 4.60: 188665 Nonbonded interactions: 474030 Sorted by model distance: nonbonded pdb=" O LYS A 528 " pdb=" H PHE A 541 " model vdw 1.670 2.450 nonbonded pdb=" O SER A 814 " pdb="HD22 ASN A 818 " model vdw 1.673 2.450 nonbonded pdb=" OE1 GLU A 827 " pdb=" H GLU A 827 " model vdw 1.682 2.450 nonbonded pdb=" O GLN A 685 " pdb=" HG1 THR A 689 " model vdw 1.688 2.450 nonbonded pdb=" O ASN A1780 " pdb="HH21 ARG A1784 " model vdw 1.689 2.450 ... (remaining 474025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.230 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 41.700 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:9.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17162 Z= 0.173 Angle : 0.553 9.155 23215 Z= 0.290 Chirality : 0.039 0.139 2561 Planarity : 0.004 0.096 2951 Dihedral : 10.379 84.529 6403 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 0.11 % Allowed : 3.27 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.16), residues: 2073 helix: -1.39 (0.14), residues: 1000 sheet: -2.69 (0.36), residues: 135 loop : -2.64 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 787 TYR 0.009 0.001 TYR A1744 PHE 0.012 0.001 PHE A1973 TRP 0.010 0.001 TRP A 609 HIS 0.004 0.001 HIS A1296 Details of bonding type rmsd covalent geometry : bond 0.00422 (17155) covalent geometry : angle 0.54776 (23213) hydrogen bonds : bond 0.14457 ( 729) hydrogen bonds : angle 6.35805 ( 2106) metal coordination : bond 0.03180 ( 7) metal coordination : angle 8.34303 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 349 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 821 THR cc_start: 0.9159 (m) cc_final: 0.8954 (m) REVERT: A 973 LEU cc_start: 0.8470 (mp) cc_final: 0.8214 (mt) REVERT: A 1139 ILE cc_start: 0.8657 (mm) cc_final: 0.8450 (mp) REVERT: A 1172 LYS cc_start: 0.8534 (mmtm) cc_final: 0.8089 (mmmt) REVERT: A 1755 GLN cc_start: 0.7314 (mp10) cc_final: 0.6859 (mm-40) REVERT: A 2006 LYS cc_start: 0.7893 (mttm) cc_final: 0.7526 (mppt) REVERT: A 2081 GLU cc_start: 0.7180 (tt0) cc_final: 0.6668 (tt0) outliers start: 2 outliers final: 1 residues processed: 349 average time/residue: 1.4639 time to fit residues: 569.4264 Evaluate side-chains 207 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1624 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 406 HIS A 590 GLN A 613 GLN A1264 ASN A1866 GLN ** A1945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.115462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.103712 restraints weight = 82089.046| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.12 r_work: 0.3227 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 17162 Z= 0.245 Angle : 0.572 5.229 23215 Z= 0.305 Chirality : 0.042 0.141 2561 Planarity : 0.005 0.095 2951 Dihedral : 4.558 45.300 2274 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.78 % Favored : 95.18 % Rotamer: Outliers : 1.50 % Allowed : 11.40 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.17), residues: 2073 helix: -0.49 (0.16), residues: 1007 sheet: -2.29 (0.36), residues: 137 loop : -2.28 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1178 TYR 0.014 0.002 TYR A 875 PHE 0.013 0.001 PHE A 362 TRP 0.013 0.002 TRP A2013 HIS 0.005 0.001 HIS A 603 Details of bonding type rmsd covalent geometry : bond 0.00572 (17155) covalent geometry : angle 0.57161 (23213) hydrogen bonds : bond 0.04611 ( 729) hydrogen bonds : angle 4.82967 ( 2106) metal coordination : bond 0.00629 ( 7) metal coordination : angle 2.81241 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8639 (ttm) cc_final: 0.8407 (ttm) REVERT: A 262 PHE cc_start: 0.7749 (m-10) cc_final: 0.7521 (m-10) REVERT: A 483 MET cc_start: 0.8527 (mtt) cc_final: 0.8011 (mtt) REVERT: A 539 ARG cc_start: 0.8546 (mtp85) cc_final: 0.7981 (mtp85) REVERT: A 890 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.7671 (ppp) REVERT: A 973 LEU cc_start: 0.8493 (mp) cc_final: 0.8218 (mt) REVERT: A 1165 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7750 (mm-40) REVERT: A 1172 LYS cc_start: 0.8646 (mmtm) cc_final: 0.8056 (mmmt) REVERT: A 1376 ARG cc_start: 0.8360 (mtp85) cc_final: 0.8065 (mtp180) REVERT: A 1541 ASP cc_start: 0.8026 (m-30) cc_final: 0.7797 (m-30) REVERT: A 1757 ASP cc_start: 0.8462 (t0) cc_final: 0.8233 (t0) REVERT: A 2006 LYS cc_start: 0.8354 (mttm) cc_final: 0.7686 (mppt) REVERT: P 83 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7902 (mp10) outliers start: 28 outliers final: 11 residues processed: 227 average time/residue: 1.3258 time to fit residues: 339.9396 Evaluate side-chains 197 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 890 MET Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1165 GLN Chi-restraints excluded: chain A residue 1210 GLU Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1540 LYS Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1763 MET Chi-restraints excluded: chain A residue 1767 ASP Chi-restraints excluded: chain P residue 53 TYR Chi-restraints excluded: chain P residue 83 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 132 optimal weight: 5.9990 chunk 185 optimal weight: 0.0020 chunk 130 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.116236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.104569 restraints weight = 81541.263| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.11 r_work: 0.3247 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17162 Z= 0.123 Angle : 0.483 5.039 23215 Z= 0.253 Chirality : 0.038 0.142 2561 Planarity : 0.004 0.086 2951 Dihedral : 4.216 42.813 2271 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.23 % Allowed : 12.37 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.18), residues: 2073 helix: 0.19 (0.16), residues: 1016 sheet: -1.97 (0.37), residues: 137 loop : -2.03 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 670 TYR 0.010 0.001 TYR A 875 PHE 0.011 0.001 PHE A 362 TRP 0.013 0.001 TRP A 94 HIS 0.003 0.001 HIS A1324 Details of bonding type rmsd covalent geometry : bond 0.00288 (17155) covalent geometry : angle 0.48226 (23213) hydrogen bonds : bond 0.03717 ( 729) hydrogen bonds : angle 4.37487 ( 2106) metal coordination : bond 0.00458 ( 7) metal coordination : angle 2.79312 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.8534 (mtt) cc_final: 0.8033 (mtt) REVERT: A 808 CYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8284 (p) REVERT: A 973 LEU cc_start: 0.8493 (mp) cc_final: 0.8240 (mt) REVERT: A 1050 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: A 1165 GLN cc_start: 0.7993 (mp10) cc_final: 0.7770 (mm-40) REVERT: A 1172 LYS cc_start: 0.8600 (mmtm) cc_final: 0.8031 (mmmt) REVERT: A 1376 ARG cc_start: 0.8339 (mtp85) cc_final: 0.8116 (mtp180) REVERT: A 1540 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.6698 (pptt) REVERT: A 1541 ASP cc_start: 0.7993 (m-30) cc_final: 0.7745 (m-30) REVERT: A 1757 ASP cc_start: 0.8504 (t0) cc_final: 0.8239 (t0) REVERT: A 1763 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7439 (ptp) REVERT: A 2006 LYS cc_start: 0.8241 (mttm) cc_final: 0.7624 (mppt) REVERT: A 2103 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7999 (mm-30) REVERT: P 83 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7916 (mp10) outliers start: 23 outliers final: 9 residues processed: 214 average time/residue: 1.2150 time to fit residues: 294.6310 Evaluate side-chains 197 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1291 CYS Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1540 LYS Chi-restraints excluded: chain A residue 1763 MET Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 2043 VAL Chi-restraints excluded: chain A residue 2103 GLU Chi-restraints excluded: chain P residue 53 TYR Chi-restraints excluded: chain P residue 83 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 163 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 170 optimal weight: 0.0470 chunk 162 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 932 ASN A1048 HIS A1870 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.113144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.101570 restraints weight = 82357.654| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.06 r_work: 0.3204 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17162 Z= 0.172 Angle : 0.509 5.437 23215 Z= 0.267 Chirality : 0.040 0.141 2561 Planarity : 0.004 0.084 2951 Dihedral : 4.264 42.847 2271 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.25 % Allowed : 11.88 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.18), residues: 2073 helix: 0.50 (0.17), residues: 1016 sheet: -1.69 (0.39), residues: 137 loop : -1.85 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 684 TYR 0.016 0.001 TYR A1941 PHE 0.010 0.001 PHE A 362 TRP 0.013 0.001 TRP A 94 HIS 0.004 0.001 HIS A1296 Details of bonding type rmsd covalent geometry : bond 0.00405 (17155) covalent geometry : angle 0.50843 (23213) hydrogen bonds : bond 0.03800 ( 729) hydrogen bonds : angle 4.27477 ( 2106) metal coordination : bond 0.00428 ( 7) metal coordination : angle 2.16008 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 199 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 PHE cc_start: 0.7799 (m-10) cc_final: 0.7596 (m-10) REVERT: A 483 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8131 (mtt) REVERT: A 808 CYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8346 (p) REVERT: A 978 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7340 (mt0) REVERT: A 1165 GLN cc_start: 0.8008 (mp10) cc_final: 0.7731 (mm-40) REVERT: A 1172 LYS cc_start: 0.8639 (mmtm) cc_final: 0.8010 (mmmt) REVERT: A 1251 MET cc_start: 0.8215 (ptp) cc_final: 0.7976 (ptm) REVERT: A 1376 ARG cc_start: 0.8355 (mtp85) cc_final: 0.8023 (mtp180) REVERT: A 1540 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.6771 (pptt) REVERT: A 1541 ASP cc_start: 0.8054 (m-30) cc_final: 0.7801 (m-30) REVERT: A 1624 MET cc_start: 0.7862 (pmt) cc_final: 0.7558 (pmt) REVERT: A 1757 ASP cc_start: 0.8636 (t0) cc_final: 0.8369 (t0) REVERT: A 1870 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7007 (tt0) REVERT: A 1960 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7694 (mp) REVERT: A 2006 LYS cc_start: 0.8283 (mttm) cc_final: 0.7679 (mppt) REVERT: P 83 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7933 (mp10) outliers start: 42 outliers final: 13 residues processed: 225 average time/residue: 1.2506 time to fit residues: 316.8233 Evaluate side-chains 203 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1291 CYS Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1540 LYS Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1763 MET Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 1870 GLN Chi-restraints excluded: chain A residue 1960 ILE Chi-restraints excluded: chain A residue 2043 VAL Chi-restraints excluded: chain P residue 53 TYR Chi-restraints excluded: chain P residue 83 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 121 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 HIS A1870 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.114526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.102847 restraints weight = 82385.795| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.10 r_work: 0.3232 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17162 Z= 0.113 Angle : 0.475 5.716 23215 Z= 0.248 Chirality : 0.038 0.144 2561 Planarity : 0.004 0.084 2951 Dihedral : 4.147 43.021 2271 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.61 % Allowed : 12.79 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.19), residues: 2073 helix: 0.76 (0.17), residues: 1016 sheet: -1.49 (0.40), residues: 137 loop : -1.71 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 684 TYR 0.013 0.001 TYR A1941 PHE 0.009 0.001 PHE A 842 TRP 0.013 0.001 TRP A 94 HIS 0.003 0.001 HIS A1324 Details of bonding type rmsd covalent geometry : bond 0.00266 (17155) covalent geometry : angle 0.47450 (23213) hydrogen bonds : bond 0.03446 ( 729) hydrogen bonds : angle 4.14366 ( 2106) metal coordination : bond 0.00610 ( 7) metal coordination : angle 2.26162 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8135 (mtt) REVERT: A 502 LYS cc_start: 0.8467 (pttt) cc_final: 0.7955 (ttmt) REVERT: A 535 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8116 (mtpm) REVERT: A 978 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7433 (mt0) REVERT: A 1050 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: A 1165 GLN cc_start: 0.8014 (mp10) cc_final: 0.7733 (mm-40) REVERT: A 1172 LYS cc_start: 0.8579 (mmtm) cc_final: 0.7993 (mmmt) REVERT: A 1376 ARG cc_start: 0.8323 (mtp85) cc_final: 0.8044 (mtp180) REVERT: A 1540 LYS cc_start: 0.7431 (pmmt) cc_final: 0.6827 (pptt) REVERT: A 1541 ASP cc_start: 0.8007 (m-30) cc_final: 0.7752 (m-30) REVERT: A 1596 MET cc_start: 0.7163 (mmt) cc_final: 0.6924 (mmt) REVERT: A 1757 ASP cc_start: 0.8657 (t0) cc_final: 0.8403 (t0) REVERT: A 1763 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.7260 (ptp) REVERT: A 1960 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7603 (mp) REVERT: A 2006 LYS cc_start: 0.8278 (mttm) cc_final: 0.7674 (mppt) REVERT: P 83 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7953 (mp10) outliers start: 30 outliers final: 11 residues processed: 212 average time/residue: 1.3235 time to fit residues: 317.6362 Evaluate side-chains 201 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1763 MET Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 1960 ILE Chi-restraints excluded: chain A residue 2043 VAL Chi-restraints excluded: chain P residue 53 TYR Chi-restraints excluded: chain P residue 83 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 200 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 190 optimal weight: 0.5980 chunk 184 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1264 ASN ** A1870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.111935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.100896 restraints weight = 83108.262| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.01 r_work: 0.3203 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17162 Z= 0.162 Angle : 0.500 6.025 23215 Z= 0.263 Chirality : 0.039 0.142 2561 Planarity : 0.004 0.084 2951 Dihedral : 4.230 43.817 2271 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.87 % Allowed : 13.17 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.19), residues: 2073 helix: 0.82 (0.17), residues: 1016 sheet: -1.33 (0.41), residues: 137 loop : -1.64 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 684 TYR 0.020 0.001 TYR A1941 PHE 0.010 0.001 PHE A 362 TRP 0.012 0.001 TRP A 94 HIS 0.004 0.001 HIS A1296 Details of bonding type rmsd covalent geometry : bond 0.00383 (17155) covalent geometry : angle 0.50000 (23213) hydrogen bonds : bond 0.03704 ( 729) hydrogen bonds : angle 4.17379 ( 2106) metal coordination : bond 0.00363 ( 7) metal coordination : angle 2.08880 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 PHE cc_start: 0.7858 (m-10) cc_final: 0.7638 (m-10) REVERT: A 483 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8179 (mtt) REVERT: A 502 LYS cc_start: 0.8492 (pttt) cc_final: 0.8046 (ttmt) REVERT: A 978 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7414 (mt0) REVERT: A 1165 GLN cc_start: 0.7961 (mp10) cc_final: 0.7700 (mm-40) REVERT: A 1172 LYS cc_start: 0.8592 (mmtm) cc_final: 0.8318 (mmmt) REVERT: A 1251 MET cc_start: 0.8251 (ptp) cc_final: 0.7983 (ptm) REVERT: A 1376 ARG cc_start: 0.8352 (mtp85) cc_final: 0.8089 (mtp180) REVERT: A 1540 LYS cc_start: 0.7451 (pmmt) cc_final: 0.6892 (pptt) REVERT: A 1541 ASP cc_start: 0.7972 (m-30) cc_final: 0.7711 (m-30) REVERT: A 1596 MET cc_start: 0.7287 (mmt) cc_final: 0.7024 (mmt) REVERT: A 1636 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7803 (tt) REVERT: A 1757 ASP cc_start: 0.8686 (t0) cc_final: 0.8418 (t0) REVERT: A 1960 ILE cc_start: 0.8139 (mt) cc_final: 0.7783 (mp) REVERT: A 2006 LYS cc_start: 0.8267 (mttm) cc_final: 0.7698 (mppt) REVERT: A 2081 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7625 (mt-10) REVERT: P 83 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7980 (mp10) outliers start: 35 outliers final: 13 residues processed: 210 average time/residue: 1.3927 time to fit residues: 329.8014 Evaluate side-chains 198 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1264 ASN Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1763 MET Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 2043 VAL Chi-restraints excluded: chain P residue 83 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 17 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 206 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1870 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.111970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.100949 restraints weight = 83298.316| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.02 r_work: 0.3203 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17162 Z= 0.150 Angle : 0.495 6.157 23215 Z= 0.260 Chirality : 0.039 0.139 2561 Planarity : 0.004 0.085 2951 Dihedral : 4.236 43.966 2271 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.77 % Allowed : 13.49 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.19), residues: 2073 helix: 0.88 (0.17), residues: 1016 sheet: -1.16 (0.42), residues: 138 loop : -1.59 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 684 TYR 0.023 0.001 TYR A1941 PHE 0.015 0.001 PHE A1265 TRP 0.012 0.001 TRP A 94 HIS 0.003 0.001 HIS A1296 Details of bonding type rmsd covalent geometry : bond 0.00352 (17155) covalent geometry : angle 0.49455 (23213) hydrogen bonds : bond 0.03613 ( 729) hydrogen bonds : angle 4.14951 ( 2106) metal coordination : bond 0.00382 ( 7) metal coordination : angle 2.04828 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 PHE cc_start: 0.7853 (m-10) cc_final: 0.7651 (m-10) REVERT: A 483 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8180 (mtt) REVERT: A 502 LYS cc_start: 0.8486 (pttt) cc_final: 0.8045 (ttmt) REVERT: A 877 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8405 (tpt) REVERT: A 978 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7361 (mt0) REVERT: A 1050 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: A 1078 MET cc_start: 0.8217 (tpt) cc_final: 0.7967 (tpt) REVERT: A 1172 LYS cc_start: 0.8594 (mmtm) cc_final: 0.8324 (mmmt) REVERT: A 1376 ARG cc_start: 0.8328 (mtp85) cc_final: 0.8077 (mtp180) REVERT: A 1540 LYS cc_start: 0.7466 (pmmt) cc_final: 0.6950 (pptt) REVERT: A 1541 ASP cc_start: 0.7881 (m-30) cc_final: 0.7599 (m-30) REVERT: A 1596 MET cc_start: 0.7293 (mmt) cc_final: 0.7009 (mmt) REVERT: A 1636 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7816 (tt) REVERT: A 1702 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8231 (mtt) REVERT: A 1757 ASP cc_start: 0.8712 (t0) cc_final: 0.8479 (t0) REVERT: A 1960 ILE cc_start: 0.8140 (mt) cc_final: 0.7785 (mp) REVERT: A 2006 LYS cc_start: 0.8262 (mttm) cc_final: 0.7725 (mppt) REVERT: A 2081 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7608 (mt-10) REVERT: P 83 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7964 (mp10) outliers start: 33 outliers final: 13 residues processed: 203 average time/residue: 1.3864 time to fit residues: 316.7462 Evaluate side-chains 200 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 877 MET Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1702 MET Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1763 MET Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 2043 VAL Chi-restraints excluded: chain P residue 53 TYR Chi-restraints excluded: chain P residue 83 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 4 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 175 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1870 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.112329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.101283 restraints weight = 82871.270| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.02 r_work: 0.3211 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17162 Z= 0.132 Angle : 0.483 5.922 23215 Z= 0.252 Chirality : 0.039 0.141 2561 Planarity : 0.004 0.084 2951 Dihedral : 4.174 43.282 2271 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.87 % Allowed : 13.33 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.19), residues: 2073 helix: 1.01 (0.17), residues: 1009 sheet: -1.09 (0.43), residues: 138 loop : -1.42 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 684 TYR 0.023 0.001 TYR A1941 PHE 0.009 0.001 PHE A 362 TRP 0.012 0.001 TRP A 94 HIS 0.003 0.001 HIS A1324 Details of bonding type rmsd covalent geometry : bond 0.00311 (17155) covalent geometry : angle 0.48255 (23213) hydrogen bonds : bond 0.03470 ( 729) hydrogen bonds : angle 4.09073 ( 2106) metal coordination : bond 0.00510 ( 7) metal coordination : angle 2.13248 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8154 (mtt) REVERT: A 502 LYS cc_start: 0.8488 (pttt) cc_final: 0.8059 (ttmt) REVERT: A 720 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8162 (p) REVERT: A 877 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8403 (tpt) REVERT: A 978 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7306 (mt0) REVERT: A 1050 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: A 1078 MET cc_start: 0.8223 (tpt) cc_final: 0.7965 (tpt) REVERT: A 1172 LYS cc_start: 0.8587 (mmtm) cc_final: 0.8322 (mmmt) REVERT: A 1376 ARG cc_start: 0.8323 (mtp85) cc_final: 0.8089 (mtp180) REVERT: A 1540 LYS cc_start: 0.7446 (pmmt) cc_final: 0.6939 (pptt) REVERT: A 1541 ASP cc_start: 0.7878 (m-30) cc_final: 0.7655 (m-30) REVERT: A 1636 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7834 (tt) REVERT: A 1702 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8235 (mtt) REVERT: A 1757 ASP cc_start: 0.8699 (t0) cc_final: 0.8471 (t0) REVERT: A 1960 ILE cc_start: 0.8093 (mt) cc_final: 0.7740 (mp) REVERT: A 2006 LYS cc_start: 0.8253 (mttm) cc_final: 0.7718 (mppt) REVERT: A 2081 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7619 (mt-10) REVERT: A 2103 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8116 (mm-30) REVERT: P 83 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8009 (mp10) outliers start: 35 outliers final: 11 residues processed: 211 average time/residue: 1.2831 time to fit residues: 307.2313 Evaluate side-chains 199 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 877 MET Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1702 MET Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1763 MET Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 2043 VAL Chi-restraints excluded: chain A residue 2103 GLU Chi-restraints excluded: chain P residue 83 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 200 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 chunk 166 optimal weight: 0.4980 chunk 142 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1870 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.114985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.103093 restraints weight = 83060.266| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.13 r_work: 0.3231 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17162 Z= 0.094 Angle : 0.465 5.759 23215 Z= 0.242 Chirality : 0.038 0.143 2561 Planarity : 0.004 0.084 2951 Dihedral : 4.012 41.579 2271 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.12 % Allowed : 14.56 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.19), residues: 2073 helix: 1.20 (0.17), residues: 1011 sheet: -1.05 (0.43), residues: 138 loop : -1.31 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 684 TYR 0.016 0.001 TYR A1941 PHE 0.008 0.001 PHE A 362 TRP 0.012 0.001 TRP A 94 HIS 0.006 0.000 HIS A1324 Details of bonding type rmsd covalent geometry : bond 0.00221 (17155) covalent geometry : angle 0.46493 (23213) hydrogen bonds : bond 0.03157 ( 729) hydrogen bonds : angle 3.97998 ( 2106) metal coordination : bond 0.00810 ( 7) metal coordination : angle 2.33595 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 PHE cc_start: 0.7805 (m-10) cc_final: 0.7578 (m-10) REVERT: A 483 MET cc_start: 0.8676 (mtt) cc_final: 0.8191 (mtt) REVERT: A 502 LYS cc_start: 0.8460 (pttt) cc_final: 0.8027 (ttmt) REVERT: A 720 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8157 (p) REVERT: A 877 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8386 (tpt) REVERT: A 978 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7379 (mt0) REVERT: A 1050 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: A 1078 MET cc_start: 0.8207 (tpt) cc_final: 0.7957 (tpt) REVERT: A 1172 LYS cc_start: 0.8570 (mmtm) cc_final: 0.7965 (mmmt) REVERT: A 1376 ARG cc_start: 0.8266 (mtp85) cc_final: 0.7939 (mtp180) REVERT: A 1383 ASP cc_start: 0.8041 (m-30) cc_final: 0.7559 (p0) REVERT: A 1540 LYS cc_start: 0.7404 (pmmt) cc_final: 0.6908 (pptt) REVERT: A 1596 MET cc_start: 0.7187 (mmt) cc_final: 0.6814 (mmt) REVERT: A 1636 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7682 (tt) REVERT: A 1683 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8362 (tp30) REVERT: A 1702 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8228 (mtt) REVERT: A 1757 ASP cc_start: 0.8689 (t0) cc_final: 0.8452 (t0) REVERT: A 1763 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7097 (ptp) REVERT: A 1775 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7345 (mt-10) REVERT: A 1870 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.6807 (tt0) REVERT: A 1960 ILE cc_start: 0.7874 (mt) cc_final: 0.7522 (mp) REVERT: A 2006 LYS cc_start: 0.8199 (mttm) cc_final: 0.7635 (mppt) REVERT: A 2081 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7573 (mt-10) REVERT: A 2103 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8102 (mm-30) REVERT: P 83 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8002 (mp10) outliers start: 21 outliers final: 5 residues processed: 208 average time/residue: 1.2503 time to fit residues: 295.4671 Evaluate side-chains 194 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 877 MET Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1702 MET Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1763 MET Chi-restraints excluded: chain A residue 1870 GLN Chi-restraints excluded: chain A residue 2043 VAL Chi-restraints excluded: chain A residue 2103 GLU Chi-restraints excluded: chain P residue 83 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 63, in __init__ refine_object.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.1196 > 50: distance: 240 - 301: 3.084 distance: 1115 - 1168: 3.034 distance: 1858 - 1925: 3.008 distance: 1979 - 2054: 3.051 distance: 2661 - 2851: 3.048 distance: 2958 - 3056: 3.106 distance: 3027 - 3029: 3.449 distance: 3029 - 3040: 4.403 distance: 3628 - 3688: 3.039 distance: 3876 - 3945: 3.069 distance: 4030 - 4090: 3.066 distance: 4300 - 4365: 3.093 distance: 5840 - 5889: 3.096 distance: 5990 - 6055: 3.030 distance: 6007 - 6067: 3.023 distance: 6660 - 6720: 3.206 distance: 7526 - 7590: 3.276 distance: 7545 - 7609: 4.067 distance: 7580 - 7588: 4.218 distance: 7722 - 7795: 3.023 distance: 7744 - 7817: 3.315 distance: 7819 - 7832: 3.132 distance: 7820 - 7878: 3.526 distance: 7822 - 7823: 3.676 distance: 7822 - 7831: 3.674 distance: 7823 - 7825: 5.087 distance: 7884 - 7893: 4.092 distance: 7951 - 7952: 3.252 distance: 7955 - 7956: 10.191 distance: 7955 - 7957: 9.072 distance: 8364 - 8450: 3.034 distance: 8429 - 8506: 3.012 distance: 8942 - 8950: 6.041 distance: 8944 - 9021: 3.005 distance: 8946 - 8948: 3.123 distance: 8948 - 8959: 3.852 distance: 8963 - 9040: 3.024 distance: 10150 - 10153: 3.013 distance: 10197 - 10318: 3.019 distance: 11767 - 11814: 3.051 distance: 11913 - 11923: 3.212 distance: 11916 - 11917: 5.201 distance: 11916 - 11918: 5.553 distance: 11923 - 11924: 7.232 distance: 11924 - 11925: 8.653 distance: 11924 - 11927: 8.493 distance: 11924 - 11932: 4.673 distance: 11927 - 11928: 4.684 distance: 11927 - 11933: 3.017 distance: 11927 - 11934: 4.376 distance: 12055 - 12168: 3.021 distance: 12341 - 12422: 3.009 distance: 12898 - 12901: 5.155 distance: 12901 - 12902: 5.200 distance: 12901 - 12908: 4.427 distance: 12902 - 12903: 7.800 distance: 12902 - 12904: 5.059 distance: 12904 - 12909: 4.643 distance: 12904 - 12910: 4.509 distance: 12926 - 12927: 3.001 distance: 12926 - 12929: 4.720 distance: 12928 - 12985: 3.329 distance: 12929 - 12930: 4.928 distance: 12929 - 12931: 4.597 distance: 12929 - 12935: 3.073 distance: 12930 - 12932: 6.995 distance: 12930 - 12936: 14.739 distance: 12930 - 12937: 8.852 distance: 12932 - 12941: 3.336 distance: 12988 - 13056: 3.295 distance: 13059 - 13118: 3.016 distance: 13151 - 13229: 3.340 distance: 13175 - 13246: 3.045 distance: 13230 - 13233: 3.767 distance: 13716 - 13718: 4.635 distance: 13718 - 13727: 3.633 distance: 13718 - 13729: 6.129 distance: 13736 - 13738: 3.199 distance: 14431 - 14501: 3.099 distance: 14450 - 14512: 3.020 distance: 14756 - 14825: 3.041 distance: 14787 - 14856: 3.249 distance: 14858 - 14859: 3.018 distance: 15167 - 15238: 3.228 distance: 15189 - 15257: 4.850 distance: 15211 - 15272: 4.406 distance: 15239 - 15240: 3.010 distance: 15257 - 15258: 3.302 distance: 15258 - 15259: 7.196 distance: 15259 - 15260: 7.499 distance: 15259 - 15272: 6.151 distance: 15262 - 15263: 6.414 distance: 15263 - 15264: 4.477 distance: 15263 - 15265: 19.255 distance: 15272 - 15273: 4.334 distance: 15272 - 15278: 4.205 distance: 15508 - 15585: 3.097 distance: 15830 - 15831: 3.329 distance: 16272 - 16337: 3.014 distance: 16283 - 16361: 3.191 distance: 16571 - 16630: 3.006 distance: 16595 - 16670: 3.076 distance: 16770 - 16832: 3.014 distance: 17106 - 17158: 3.005 distance: 17161 - 17236: 3.005 distance: 17838 - 19572: 3.080 distance: 18158 - 18159: 3.302 distance: 18159 - 18170: 4.240 distance: 18500 - 18567: 3.019 distance: 18613 - 18656: 3.046 distance: 18932 - 18990: 3.064 distance: 18946 - 19009: 3.382 distance: 19573 - 19580: 4.418 distance: 19576 - 19584: 3.407 distance: 19670 - 19722: 3.026 distance: 19706 - 19741: 3.088 distance: 20475 - 20485: 3.239 distance: 20685 - 20686: 8.263 distance: 20685 - 20695: 3.452 distance: 20686 - 20687: 8.438 distance: 20686 - 20689: 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