Starting phenix.real_space_refine on Tue May 27 21:48:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t9j_10413/05_2025/6t9j_10413.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t9j_10413/05_2025/6t9j_10413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t9j_10413/05_2025/6t9j_10413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t9j_10413/05_2025/6t9j_10413.map" model { file = "/net/cci-nas-00/data/ceres_data/6t9j_10413/05_2025/6t9j_10413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t9j_10413/05_2025/6t9j_10413.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 19112 2.51 5 N 4919 2.21 5 O 5395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 172 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29550 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 365 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain breaks: 1 Chain: "I" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 456 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 8, 'TRANS': 52} Chain: "T" Number of atoms: 28729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3513, 28729 Classifications: {'peptide': 3513} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 149, 'TRANS': 3363} Chain breaks: 11 Time building chain proxies: 15.79, per 1000 atoms: 0.53 Number of scatterers: 29550 At special positions: 0 Unit cell: (136.5, 176.4, 170.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 5395 8.00 N 4919 7.00 C 19112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.24 Conformation dependent library (CDL) restraints added in 3.2 seconds 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7064 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 4 sheets defined 66.2% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.44 Creating SS restraints... Processing helix chain 'B' and resid 403 through 413 Processing helix chain 'B' and resid 475 through 488 Processing helix chain 'T' and resid 3 through 10 removed outlier: 3.733A pdb=" N GLN T 6 " --> pdb=" O LEU T 3 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU T 8 " --> pdb=" O GLU T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 31 removed outlier: 3.778A pdb=" N GLU T 30 " --> pdb=" O THR T 27 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU T 31 " --> pdb=" O LEU T 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 27 through 31' Processing helix chain 'T' and resid 44 through 61 removed outlier: 4.149A pdb=" N GLN T 49 " --> pdb=" O HIS T 45 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ALA T 50 " --> pdb=" O PHE T 46 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE T 52 " --> pdb=" O LEU T 48 " (cutoff:3.500A) Proline residue: T 53 - end of helix removed outlier: 4.287A pdb=" N GLU T 61 " --> pdb=" O ASN T 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 72 through 86 removed outlier: 3.518A pdb=" N ASN T 84 " --> pdb=" O LEU T 80 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG T 85 " --> pdb=" O ASP T 81 " (cutoff:3.500A) Processing helix chain 'T' and resid 91 through 97 removed outlier: 3.998A pdb=" N TYR T 95 " --> pdb=" O THR T 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 104 removed outlier: 3.941A pdb=" N LEU T 103 " --> pdb=" O VAL T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 117 through 132 removed outlier: 4.586A pdb=" N THR T 123 " --> pdb=" O MET T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 141 through 157 removed outlier: 3.888A pdb=" N ILE T 145 " --> pdb=" O ILE T 141 " (cutoff:3.500A) Proline residue: T 152 - end of helix Processing helix chain 'T' and resid 231 through 240 Processing helix chain 'T' and resid 250 through 254 removed outlier: 3.535A pdb=" N ILE T 253 " --> pdb=" O THR T 250 " (cutoff:3.500A) Processing helix chain 'T' and resid 293 through 309 Processing helix chain 'T' and resid 310 through 314 Processing helix chain 'T' and resid 324 through 335 removed outlier: 3.826A pdb=" N LEU T 328 " --> pdb=" O PHE T 324 " (cutoff:3.500A) Processing helix chain 'T' and resid 341 through 356 removed outlier: 4.072A pdb=" N LYS T 345 " --> pdb=" O SER T 341 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU T 346 " --> pdb=" O SER T 342 " (cutoff:3.500A) Processing helix chain 'T' and resid 363 through 369 Processing helix chain 'T' and resid 374 through 378 Processing helix chain 'T' and resid 387 through 403 Processing helix chain 'T' and resid 407 through 424 removed outlier: 3.628A pdb=" N ILE T 417 " --> pdb=" O LYS T 413 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY T 420 " --> pdb=" O LYS T 416 " (cutoff:3.500A) Processing helix chain 'T' and resid 428 through 453 removed outlier: 3.696A pdb=" N GLN T 432 " --> pdb=" O ALA T 428 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU T 444 " --> pdb=" O LEU T 440 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG T 445 " --> pdb=" O ASN T 441 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN T 453 " --> pdb=" O LEU T 449 " (cutoff:3.500A) Processing helix chain 'T' and resid 456 through 480 removed outlier: 3.711A pdb=" N LEU T 463 " --> pdb=" O ARG T 459 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE T 468 " --> pdb=" O LEU T 464 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP T 469 " --> pdb=" O MET T 465 " (cutoff:3.500A) Processing helix chain 'T' and resid 481 through 498 removed outlier: 3.704A pdb=" N LYS T 496 " --> pdb=" O TYR T 492 " (cutoff:3.500A) Processing helix chain 'T' and resid 512 through 520 Processing helix chain 'T' and resid 561 through 567 removed outlier: 3.698A pdb=" N LYS T 564 " --> pdb=" O PHE T 561 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA T 567 " --> pdb=" O LYS T 564 " (cutoff:3.500A) Processing helix chain 'T' and resid 578 through 601 Processing helix chain 'T' and resid 602 through 605 removed outlier: 4.016A pdb=" N ASN T 605 " --> pdb=" O LYS T 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 602 through 605' Processing helix chain 'T' and resid 627 through 644 removed outlier: 4.060A pdb=" N VAL T 633 " --> pdb=" O GLU T 629 " (cutoff:3.500A) Processing helix chain 'T' and resid 645 through 647 No H-bonds generated for 'chain 'T' and resid 645 through 647' Processing helix chain 'T' and resid 676 through 690 removed outlier: 3.560A pdb=" N PHE T 690 " --> pdb=" O LEU T 686 " (cutoff:3.500A) Processing helix chain 'T' and resid 694 through 714 removed outlier: 4.090A pdb=" N GLU T 700 " --> pdb=" O ALA T 696 " (cutoff:3.500A) Proline residue: T 707 - end of helix Processing helix chain 'T' and resid 716 through 718 No H-bonds generated for 'chain 'T' and resid 716 through 718' Processing helix chain 'T' and resid 719 through 728 removed outlier: 3.681A pdb=" N ALA T 723 " --> pdb=" O LEU T 719 " (cutoff:3.500A) Processing helix chain 'T' and resid 732 through 748 removed outlier: 3.794A pdb=" N GLY T 746 " --> pdb=" O ARG T 742 " (cutoff:3.500A) Processing helix chain 'T' and resid 749 through 751 No H-bonds generated for 'chain 'T' and resid 749 through 751' Processing helix chain 'T' and resid 755 through 776 removed outlier: 3.914A pdb=" N VAL T 773 " --> pdb=" O SER T 769 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN T 774 " --> pdb=" O PHE T 770 " (cutoff:3.500A) Processing helix chain 'T' and resid 788 through 799 Processing helix chain 'T' and resid 806 through 819 removed outlier: 3.556A pdb=" N ILE T 819 " --> pdb=" O LEU T 815 " (cutoff:3.500A) Processing helix chain 'T' and resid 827 through 830 removed outlier: 4.007A pdb=" N SER T 830 " --> pdb=" O LEU T 827 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 827 through 830' Processing helix chain 'T' and resid 831 through 844 removed outlier: 3.574A pdb=" N LEU T 842 " --> pdb=" O LEU T 838 " (cutoff:3.500A) Processing helix chain 'T' and resid 853 through 863 removed outlier: 3.500A pdb=" N ILE T 863 " --> pdb=" O VAL T 859 " (cutoff:3.500A) Processing helix chain 'T' and resid 879 through 889 removed outlier: 3.572A pdb=" N VAL T 884 " --> pdb=" O MET T 880 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE T 885 " --> pdb=" O LYS T 881 " (cutoff:3.500A) Processing helix chain 'T' and resid 893 through 907 removed outlier: 3.823A pdb=" N ARG T 899 " --> pdb=" O SER T 895 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN T 907 " --> pdb=" O LEU T 903 " (cutoff:3.500A) Processing helix chain 'T' and resid 917 through 919 No H-bonds generated for 'chain 'T' and resid 917 through 919' Processing helix chain 'T' and resid 920 through 929 Processing helix chain 'T' and resid 930 through 932 No H-bonds generated for 'chain 'T' and resid 930 through 932' Processing helix chain 'T' and resid 942 through 952 Processing helix chain 'T' and resid 996 through 1006 removed outlier: 3.606A pdb=" N SER T1006 " --> pdb=" O ASN T1002 " (cutoff:3.500A) Processing helix chain 'T' and resid 1010 through 1031 removed outlier: 3.621A pdb=" N ARG T1014 " --> pdb=" O ASP T1010 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER T1031 " --> pdb=" O LEU T1027 " (cutoff:3.500A) Processing helix chain 'T' and resid 1038 through 1049 Processing helix chain 'T' and resid 1068 through 1089 Processing helix chain 'T' and resid 1090 through 1092 No H-bonds generated for 'chain 'T' and resid 1090 through 1092' Processing helix chain 'T' and resid 1095 through 1121 removed outlier: 3.561A pdb=" N ALA T1099 " --> pdb=" O LEU T1095 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU T1112 " --> pdb=" O ASP T1108 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL T1115 " --> pdb=" O CYS T1111 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN T1116 " --> pdb=" O LEU T1112 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR T1117 " --> pdb=" O LEU T1113 " (cutoff:3.500A) Processing helix chain 'T' and resid 1122 through 1124 No H-bonds generated for 'chain 'T' and resid 1122 through 1124' Processing helix chain 'T' and resid 1148 through 1154 removed outlier: 3.625A pdb=" N SER T1154 " --> pdb=" O PRO T1150 " (cutoff:3.500A) Processing helix chain 'T' and resid 1157 through 1180 removed outlier: 3.745A pdb=" N VAL T1163 " --> pdb=" O GLU T1159 " (cutoff:3.500A) Processing helix chain 'T' and resid 1180 through 1185 removed outlier: 4.084A pdb=" N LEU T1185 " --> pdb=" O GLU T1181 " (cutoff:3.500A) Processing helix chain 'T' and resid 1188 through 1201 removed outlier: 4.044A pdb=" N GLU T1192 " --> pdb=" O SER T1188 " (cutoff:3.500A) Processing helix chain 'T' and resid 1205 through 1223 removed outlier: 3.549A pdb=" N LYS T1209 " --> pdb=" O THR T1205 " (cutoff:3.500A) Processing helix chain 'T' and resid 1228 through 1233 Processing helix chain 'T' and resid 1233 through 1247 removed outlier: 3.687A pdb=" N LEU T1245 " --> pdb=" O LEU T1241 " (cutoff:3.500A) Processing helix chain 'T' and resid 1254 through 1272 Processing helix chain 'T' and resid 1283 through 1294 removed outlier: 3.591A pdb=" N ASN T1287 " --> pdb=" O LYS T1283 " (cutoff:3.500A) Processing helix chain 'T' and resid 1300 through 1313 removed outlier: 3.531A pdb=" N ARG T1304 " --> pdb=" O ASN T1300 " (cutoff:3.500A) Processing helix chain 'T' and resid 1321 through 1326 Processing helix chain 'T' and resid 1329 through 1340 removed outlier: 3.517A pdb=" N LEU T1333 " --> pdb=" O SER T1329 " (cutoff:3.500A) Proline residue: T1336 - end of helix removed outlier: 3.747A pdb=" N LYS T1340 " --> pdb=" O PRO T1336 " (cutoff:3.500A) Processing helix chain 'T' and resid 1346 through 1363 removed outlier: 3.571A pdb=" N LEU T1363 " --> pdb=" O PHE T1359 " (cutoff:3.500A) Processing helix chain 'T' and resid 1371 through 1383 removed outlier: 3.518A pdb=" N PHE T1375 " --> pdb=" O ASN T1371 " (cutoff:3.500A) Processing helix chain 'T' and resid 1404 through 1424 Processing helix chain 'T' and resid 1436 through 1447 removed outlier: 3.734A pdb=" N VAL T1443 " --> pdb=" O ARG T1439 " (cutoff:3.500A) Processing helix chain 'T' and resid 1452 through 1467 removed outlier: 3.514A pdb=" N ILE T1456 " --> pdb=" O SER T1452 " (cutoff:3.500A) Processing helix chain 'T' and resid 1468 through 1470 No H-bonds generated for 'chain 'T' and resid 1468 through 1470' Processing helix chain 'T' and resid 1477 through 1482 removed outlier: 3.937A pdb=" N LEU T1482 " --> pdb=" O LEU T1478 " (cutoff:3.500A) Processing helix chain 'T' and resid 1482 through 1489 Processing helix chain 'T' and resid 1496 through 1508 Processing helix chain 'T' and resid 1517 through 1528 Processing helix chain 'T' and resid 1532 through 1538 removed outlier: 3.570A pdb=" N THR T1537 " --> pdb=" O GLU T1533 " (cutoff:3.500A) Processing helix chain 'T' and resid 1546 through 1558 Processing helix chain 'T' and resid 1570 through 1584 Processing helix chain 'T' and resid 1593 through 1604 removed outlier: 3.882A pdb=" N ARG T1602 " --> pdb=" O ARG T1598 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE T1603 " --> pdb=" O TYR T1599 " (cutoff:3.500A) Processing helix chain 'T' and resid 1605 through 1613 removed outlier: 3.966A pdb=" N GLU T1609 " --> pdb=" O ASN T1605 " (cutoff:3.500A) Processing helix chain 'T' and resid 1617 through 1629 removed outlier: 4.031A pdb=" N GLN T1629 " --> pdb=" O CYS T1625 " (cutoff:3.500A) Processing helix chain 'T' and resid 1633 through 1642 removed outlier: 4.137A pdb=" N GLU T1638 " --> pdb=" O LYS T1634 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS T1642 " --> pdb=" O GLU T1638 " (cutoff:3.500A) Processing helix chain 'T' and resid 1643 through 1659 Proline residue: T1656 - end of helix Processing helix chain 'T' and resid 1661 through 1679 Processing helix chain 'T' and resid 1690 through 1709 Processing helix chain 'T' and resid 1715 through 1734 removed outlier: 3.763A pdb=" N ASN T1719 " --> pdb=" O HIS T1715 " (cutoff:3.500A) Processing helix chain 'T' and resid 1739 through 1750 removed outlier: 4.079A pdb=" N LEU T1743 " --> pdb=" O ASP T1739 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU T1744 " --> pdb=" O GLN T1740 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE T1750 " --> pdb=" O ASP T1746 " (cutoff:3.500A) Processing helix chain 'T' and resid 1762 through 1770 Processing helix chain 'T' and resid 1771 through 1775 removed outlier: 3.824A pdb=" N SER T1774 " --> pdb=" O ILE T1771 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN T1775 " --> pdb=" O ALA T1772 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 1771 through 1775' Processing helix chain 'T' and resid 1777 through 1792 removed outlier: 3.507A pdb=" N ASN T1781 " --> pdb=" O GLU T1777 " (cutoff:3.500A) Processing helix chain 'T' and resid 1796 through 1817 removed outlier: 3.554A pdb=" N ILE T1800 " --> pdb=" O LEU T1796 " (cutoff:3.500A) Processing helix chain 'T' and resid 1833 through 1843 removed outlier: 3.744A pdb=" N LYS T1843 " --> pdb=" O ASN T1839 " (cutoff:3.500A) Processing helix chain 'T' and resid 1844 through 1845 No H-bonds generated for 'chain 'T' and resid 1844 through 1845' Processing helix chain 'T' and resid 1846 through 1850 Processing helix chain 'T' and resid 1858 through 1875 removed outlier: 3.546A pdb=" N PHE T1862 " --> pdb=" O ASP T1858 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP T1875 " --> pdb=" O PHE T1871 " (cutoff:3.500A) Processing helix chain 'T' and resid 1882 through 1893 removed outlier: 3.795A pdb=" N PHE T1893 " --> pdb=" O PHE T1889 " (cutoff:3.500A) Processing helix chain 'T' and resid 1899 through 1916 Processing helix chain 'T' and resid 1920 through 1931 removed outlier: 4.542A pdb=" N THR T1924 " --> pdb=" O ILE T1920 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN T1925 " --> pdb=" O LYS T1921 " (cutoff:3.500A) Processing helix chain 'T' and resid 1935 through 1937 No H-bonds generated for 'chain 'T' and resid 1935 through 1937' Processing helix chain 'T' and resid 1938 through 1958 removed outlier: 3.507A pdb=" N VAL T1942 " --> pdb=" O ALA T1938 " (cutoff:3.500A) Proline residue: T1951 - end of helix removed outlier: 3.667A pdb=" N GLU T1955 " --> pdb=" O PRO T1951 " (cutoff:3.500A) Processing helix chain 'T' and resid 1964 through 1977 removed outlier: 4.176A pdb=" N ASN T1968 " --> pdb=" O ASP T1964 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL T1970 " --> pdb=" O TRP T1966 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN T1977 " --> pdb=" O VAL T1973 " (cutoff:3.500A) Processing helix chain 'T' and resid 1982 through 1988 removed outlier: 4.359A pdb=" N TYR T1986 " --> pdb=" O ASN T1982 " (cutoff:3.500A) Processing helix chain 'T' and resid 2001 through 2015 removed outlier: 3.829A pdb=" N SER T2005 " --> pdb=" O ASP T2001 " (cutoff:3.500A) Processing helix chain 'T' and resid 2024 through 2043 removed outlier: 3.559A pdb=" N ALA T2028 " --> pdb=" O SER T2024 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP T2030 " --> pdb=" O THR T2026 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR T2037 " --> pdb=" O SER T2033 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU T2043 " --> pdb=" O GLU T2039 " (cutoff:3.500A) Processing helix chain 'T' and resid 2090 through 2107 removed outlier: 3.944A pdb=" N GLU T2094 " --> pdb=" O LEU T2090 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER T2107 " --> pdb=" O TYR T2103 " (cutoff:3.500A) Processing helix chain 'T' and resid 2116 through 2129 removed outlier: 4.205A pdb=" N SER T2129 " --> pdb=" O SER T2125 " (cutoff:3.500A) Processing helix chain 'T' and resid 2155 through 2173 removed outlier: 4.077A pdb=" N TYR T2169 " --> pdb=" O LEU T2165 " (cutoff:3.500A) Processing helix chain 'T' and resid 2183 through 2196 removed outlier: 4.646A pdb=" N LYS T2193 " --> pdb=" O ASN T2189 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N CYS T2194 " --> pdb=" O LEU T2190 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS T2196 " --> pdb=" O GLU T2192 " (cutoff:3.500A) Processing helix chain 'T' and resid 2203 through 2217 removed outlier: 5.164A pdb=" N GLN T2211 " --> pdb=" O GLN T2207 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL T2212 " --> pdb=" O LYS T2208 " (cutoff:3.500A) Processing helix chain 'T' and resid 2228 through 2245 removed outlier: 4.048A pdb=" N GLY T2232 " --> pdb=" O GLU T2228 " (cutoff:3.500A) Processing helix chain 'T' and resid 2251 through 2267 removed outlier: 4.400A pdb=" N ALA T2255 " --> pdb=" O SER T2251 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY T2256 " --> pdb=" O SER T2252 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL T2257 " --> pdb=" O VAL T2253 " (cutoff:3.500A) Processing helix chain 'T' and resid 2275 through 2290 Processing helix chain 'T' and resid 2302 through 2321 removed outlier: 3.661A pdb=" N ILE T2306 " --> pdb=" O GLU T2302 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR T2308 " --> pdb=" O ALA T2304 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE T2317 " --> pdb=" O LYS T2313 " (cutoff:3.500A) Processing helix chain 'T' and resid 2328 through 2342 removed outlier: 3.709A pdb=" N PHE T2332 " --> pdb=" O SER T2328 " (cutoff:3.500A) Processing helix chain 'T' and resid 2345 through 2361 removed outlier: 3.540A pdb=" N LEU T2349 " --> pdb=" O ASP T2345 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS T2351 " --> pdb=" O ASN T2347 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE T2361 " --> pdb=" O ARG T2357 " (cutoff:3.500A) Processing helix chain 'T' and resid 2369 through 2378 removed outlier: 3.643A pdb=" N LYS T2378 " --> pdb=" O ALA T2374 " (cutoff:3.500A) Processing helix chain 'T' and resid 2381 through 2386 Processing helix chain 'T' and resid 2387 through 2402 removed outlier: 3.520A pdb=" N SER T2391 " --> pdb=" O GLU T2387 " (cutoff:3.500A) Processing helix chain 'T' and resid 2417 through 2424 removed outlier: 3.845A pdb=" N LEU T2421 " --> pdb=" O GLU T2417 " (cutoff:3.500A) Processing helix chain 'T' and resid 2428 through 2443 removed outlier: 3.778A pdb=" N LEU T2443 " --> pdb=" O LEU T2439 " (cutoff:3.500A) Processing helix chain 'T' and resid 2446 through 2456 Processing helix chain 'T' and resid 2468 through 2477 Processing helix chain 'T' and resid 2478 through 2480 No H-bonds generated for 'chain 'T' and resid 2478 through 2480' Processing helix chain 'T' and resid 2499 through 2503 removed outlier: 3.720A pdb=" N TYR T2503 " --> pdb=" O LEU T2500 " (cutoff:3.500A) Processing helix chain 'T' and resid 2518 through 2534 removed outlier: 3.565A pdb=" N LYS T2524 " --> pdb=" O SER T2520 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY T2532 " --> pdb=" O ALA T2528 " (cutoff:3.500A) Processing helix chain 'T' and resid 2537 through 2550 removed outlier: 4.430A pdb=" N PHE T2541 " --> pdb=" O ILE T2537 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU T2547 " --> pdb=" O ASP T2543 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE T2548 " --> pdb=" O SER T2544 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE T2549 " --> pdb=" O LEU T2545 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR T2550 " --> pdb=" O ILE T2546 " (cutoff:3.500A) Processing helix chain 'T' and resid 2553 through 2568 removed outlier: 3.681A pdb=" N HIS T2557 " --> pdb=" O PRO T2553 " (cutoff:3.500A) Proline residue: T2565 - end of helix Processing helix chain 'T' and resid 2569 through 2571 No H-bonds generated for 'chain 'T' and resid 2569 through 2571' Processing helix chain 'T' and resid 2575 through 2588 Processing helix chain 'T' and resid 2589 through 2596 removed outlier: 3.798A pdb=" N HIS T2592 " --> pdb=" O LYS T2589 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR T2593 " --> pdb=" O PRO T2590 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG T2594 " --> pdb=" O TYR T2591 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE T2596 " --> pdb=" O THR T2593 " (cutoff:3.500A) Processing helix chain 'T' and resid 2601 through 2611 removed outlier: 3.834A pdb=" N SER T2609 " --> pdb=" O MET T2605 " (cutoff:3.500A) Processing helix chain 'T' and resid 2622 through 2627 Processing helix chain 'T' and resid 2632 through 2645 removed outlier: 3.676A pdb=" N ILE T2639 " --> pdb=" O GLN T2635 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE T2643 " --> pdb=" O ILE T2639 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN T2644 " --> pdb=" O LEU T2640 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER T2645 " --> pdb=" O GLU T2641 " (cutoff:3.500A) Processing helix chain 'T' and resid 2654 through 2669 Processing helix chain 'T' and resid 2671 through 2683 Processing helix chain 'T' and resid 2685 through 2698 removed outlier: 3.850A pdb=" N ASN T2689 " --> pdb=" O TYR T2685 " (cutoff:3.500A) Processing helix chain 'T' and resid 2699 through 2716 removed outlier: 3.614A pdb=" N ALA T2714 " --> pdb=" O ALA T2710 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG T2715 " --> pdb=" O GLN T2711 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER T2716 " --> pdb=" O VAL T2712 " (cutoff:3.500A) Processing helix chain 'T' and resid 2724 through 2740 removed outlier: 3.550A pdb=" N LEU T2728 " --> pdb=" O SER T2724 " (cutoff:3.500A) Processing helix chain 'T' and resid 2742 through 2753 removed outlier: 3.506A pdb=" N LEU T2746 " --> pdb=" O HIS T2742 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU T2748 " --> pdb=" O ASP T2744 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU T2753 " --> pdb=" O LEU T2749 " (cutoff:3.500A) Processing helix chain 'T' and resid 2772 through 2784 removed outlier: 3.803A pdb=" N SER T2779 " --> pdb=" O ALA T2775 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL T2783 " --> pdb=" O SER T2779 " (cutoff:3.500A) Processing helix chain 'T' and resid 2788 through 2806 Processing helix chain 'T' and resid 2812 through 2831 removed outlier: 4.060A pdb=" N ASP T2818 " --> pdb=" O ARG T2814 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU T2831 " --> pdb=" O LYS T2827 " (cutoff:3.500A) Processing helix chain 'T' and resid 2838 through 2864 removed outlier: 3.932A pdb=" N LEU T2842 " --> pdb=" O ALA T2838 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR T2864 " --> pdb=" O ALA T2860 " (cutoff:3.500A) Processing helix chain 'T' and resid 2865 through 2868 Processing helix chain 'T' and resid 2873 through 2886 removed outlier: 3.700A pdb=" N ILE T2877 " --> pdb=" O LYS T2873 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP T2886 " --> pdb=" O GLN T2882 " (cutoff:3.500A) Processing helix chain 'T' and resid 2894 through 2916 removed outlier: 3.805A pdb=" N ILE T2912 " --> pdb=" O ALA T2908 " (cutoff:3.500A) Processing helix chain 'T' and resid 2920 through 2924 removed outlier: 3.519A pdb=" N LEU T2923 " --> pdb=" O ILE T2920 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN T2924 " --> pdb=" O PRO T2921 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 2920 through 2924' Processing helix chain 'T' and resid 2942 through 2957 removed outlier: 3.791A pdb=" N VAL T2946 " --> pdb=" O GLU T2942 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE T2950 " --> pdb=" O VAL T2946 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG T2955 " --> pdb=" O ALA T2951 " (cutoff:3.500A) Processing helix chain 'T' and resid 2959 through 2966 Processing helix chain 'T' and resid 2979 through 2992 removed outlier: 3.835A pdb=" N HIS T2992 " --> pdb=" O GLN T2988 " (cutoff:3.500A) Processing helix chain 'T' and resid 2998 through 3007 removed outlier: 4.052A pdb=" N VAL T3005 " --> pdb=" O THR T3001 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE T3006 " --> pdb=" O GLY T3002 " (cutoff:3.500A) Processing helix chain 'T' and resid 3017 through 3033 removed outlier: 3.935A pdb=" N LEU T3033 " --> pdb=" O PHE T3029 " (cutoff:3.500A) Processing helix chain 'T' and resid 3036 through 3048 removed outlier: 4.003A pdb=" N ASN T3040 " --> pdb=" O TYR T3036 " (cutoff:3.500A) Processing helix chain 'T' and resid 3053 through 3069 removed outlier: 3.791A pdb=" N TRP T3057 " --> pdb=" O LEU T3053 " (cutoff:3.500A) Processing helix chain 'T' and resid 3077 through 3091 removed outlier: 3.736A pdb=" N ALA T3081 " --> pdb=" O PHE T3077 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU T3091 " --> pdb=" O GLN T3087 " (cutoff:3.500A) Processing helix chain 'T' and resid 3097 through 3109 removed outlier: 3.972A pdb=" N SER T3109 " --> pdb=" O LEU T3105 " (cutoff:3.500A) Processing helix chain 'T' and resid 3115 through 3123 removed outlier: 3.614A pdb=" N ASN T3119 " --> pdb=" O GLY T3115 " (cutoff:3.500A) Processing helix chain 'T' and resid 3130 through 3135 removed outlier: 3.972A pdb=" N THR T3135 " --> pdb=" O TYR T3132 " (cutoff:3.500A) Processing helix chain 'T' and resid 3136 through 3142 Processing helix chain 'T' and resid 3151 through 3163 removed outlier: 3.943A pdb=" N ILE T3155 " --> pdb=" O MET T3151 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER T3162 " --> pdb=" O ARG T3158 " (cutoff:3.500A) Processing helix chain 'T' and resid 3163 through 3180 removed outlier: 4.246A pdb=" N LEU T3167 " --> pdb=" O TYR T3163 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS T3168 " --> pdb=" O PRO T3164 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N PHE T3169 " --> pdb=" O GLN T3165 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLN T3170 " --> pdb=" O ALA T3166 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL T3180 " --> pdb=" O GLU T3176 " (cutoff:3.500A) Processing helix chain 'T' and resid 3203 through 3218 Processing helix chain 'T' and resid 3219 through 3237 removed outlier: 3.513A pdb=" N ALA T3223 " --> pdb=" O TYR T3219 " (cutoff:3.500A) Processing helix chain 'T' and resid 3240 through 3260 Processing helix chain 'T' and resid 3273 through 3286 removed outlier: 3.523A pdb=" N GLU T3277 " --> pdb=" O PRO T3273 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR T3285 " --> pdb=" O VAL T3281 " (cutoff:3.500A) Processing helix chain 'T' and resid 3292 through 3297 Processing helix chain 'T' and resid 3298 through 3300 No H-bonds generated for 'chain 'T' and resid 3298 through 3300' Processing helix chain 'T' and resid 3308 through 3327 Processing helix chain 'T' and resid 3333 through 3338 Processing helix chain 'T' and resid 3338 through 3343 removed outlier: 3.611A pdb=" N SER T3342 " --> pdb=" O CYS T3338 " (cutoff:3.500A) Processing helix chain 'T' and resid 3343 through 3348 removed outlier: 3.800A pdb=" N GLN T3347 " --> pdb=" O ASN T3343 " (cutoff:3.500A) Processing helix chain 'T' and resid 3412 through 3426 removed outlier: 3.511A pdb=" N GLU T3416 " --> pdb=" O HIS T3412 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE T3426 " --> pdb=" O LEU T3422 " (cutoff:3.500A) Processing helix chain 'T' and resid 3428 through 3433 removed outlier: 3.538A pdb=" N LYS T3432 " --> pdb=" O LYS T3428 " (cutoff:3.500A) Processing helix chain 'T' and resid 3433 through 3439 removed outlier: 3.634A pdb=" N ARG T3439 " --> pdb=" O GLU T3435 " (cutoff:3.500A) Processing helix chain 'T' and resid 3467 through 3478 removed outlier: 3.521A pdb=" N LYS T3478 " --> pdb=" O PHE T3474 " (cutoff:3.500A) Processing helix chain 'T' and resid 3482 through 3495 removed outlier: 4.113A pdb=" N GLN T3486 " --> pdb=" O PRO T3482 " (cutoff:3.500A) Processing helix chain 'T' and resid 3505 through 3521 removed outlier: 3.954A pdb=" N LEU T3509 " --> pdb=" O ASP T3505 " (cutoff:3.500A) Processing helix chain 'T' and resid 3525 through 3535 removed outlier: 3.685A pdb=" N PHE T3535 " --> pdb=" O PHE T3531 " (cutoff:3.500A) Processing helix chain 'T' and resid 3537 through 3561 removed outlier: 3.846A pdb=" N SER T3550 " --> pdb=" O LYS T3546 " (cutoff:3.500A) Processing helix chain 'T' and resid 3562 through 3564 No H-bonds generated for 'chain 'T' and resid 3562 through 3564' Processing helix chain 'T' and resid 3625 through 3633 Processing helix chain 'T' and resid 3634 through 3640 Processing helix chain 'T' and resid 3640 through 3654 removed outlier: 3.880A pdb=" N SER T3649 " --> pdb=" O LEU T3645 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE T3653 " --> pdb=" O SER T3649 " (cutoff:3.500A) Processing helix chain 'T' and resid 3658 through 3678 removed outlier: 4.269A pdb=" N LEU T3665 " --> pdb=" O THR T3661 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU T3670 " --> pdb=" O PHE T3666 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU T3678 " --> pdb=" O TRP T3674 " (cutoff:3.500A) Processing helix chain 'T' and resid 3685 through 3707 removed outlier: 3.679A pdb=" N ARG T3689 " --> pdb=" O ASN T3685 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU T3706 " --> pdb=" O LYS T3702 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY T3707 " --> pdb=" O VAL T3703 " (cutoff:3.500A) Processing helix chain 'T' and resid 3718 through 3727 Processing helix chain 'T' and resid 3729 through 3734 Processing sheet with id=AA1, first strand: chain 'T' and resid 977 through 980 Processing sheet with id=AA2, first strand: chain 'T' and resid 3331 through 3332 Processing sheet with id=AA3, first strand: chain 'T' and resid 3331 through 3332 removed outlier: 4.144A pdb=" N ARG T3389 " --> pdb=" O VAL T3405 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'T' and resid 3464 through 3466 1480 hydrogen bonds defined for protein. 4377 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.77 Time building geometry restraints manager: 7.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7657 1.33 - 1.46: 6761 1.46 - 1.58: 15563 1.58 - 1.70: 1 1.70 - 1.83: 211 Bond restraints: 30193 Sorted by residual: bond pdb=" C ARG T 288 " pdb=" N PRO T 289 " ideal model delta sigma weight residual 1.334 1.406 -0.072 2.34e-02 1.83e+03 9.55e+00 bond pdb=" C LEU T 851 " pdb=" N PRO T 852 " ideal model delta sigma weight residual 1.334 1.401 -0.067 2.34e-02 1.83e+03 8.17e+00 bond pdb=" CA VAL T 62 " pdb=" CB VAL T 62 " ideal model delta sigma weight residual 1.537 1.567 -0.030 1.29e-02 6.01e+03 5.42e+00 bond pdb=" C GLU T3654 " pdb=" N PRO T3655 " ideal model delta sigma weight residual 1.334 1.387 -0.054 2.34e-02 1.83e+03 5.24e+00 bond pdb=" C GLN T3203 " pdb=" N PRO T3204 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.99e+00 ... (remaining 30188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 39852 2.85 - 5.70: 861 5.70 - 8.56: 161 8.56 - 11.41: 31 11.41 - 14.26: 8 Bond angle restraints: 40913 Sorted by residual: angle pdb=" CA VAL T 62 " pdb=" CB VAL T 62 " pdb=" CG1 VAL T 62 " ideal model delta sigma weight residual 110.40 120.31 -9.91 1.70e+00 3.46e-01 3.40e+01 angle pdb=" C ILE I 385 " pdb=" N THR I 386 " pdb=" CA THR I 386 " ideal model delta sigma weight residual 126.32 134.56 -8.24 1.74e+00 3.30e-01 2.24e+01 angle pdb=" C GLN T 319 " pdb=" N ASP T 320 " pdb=" CA ASP T 320 " ideal model delta sigma weight residual 121.54 130.53 -8.99 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C ASN T1844 " pdb=" CA ASN T1844 " pdb=" CB ASN T1844 " ideal model delta sigma weight residual 110.32 100.53 9.79 2.11e+00 2.25e-01 2.15e+01 angle pdb=" CA THR T3377 " pdb=" CB THR T3377 " pdb=" CG2 THR T3377 " ideal model delta sigma weight residual 110.50 118.22 -7.72 1.70e+00 3.46e-01 2.06e+01 ... (remaining 40908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16271 17.95 - 35.91: 1736 35.91 - 53.86: 276 53.86 - 71.81: 74 71.81 - 89.77: 19 Dihedral angle restraints: 18376 sinusoidal: 7578 harmonic: 10798 Sorted by residual: dihedral pdb=" CA HIS T2621 " pdb=" C HIS T2621 " pdb=" N LEU T2622 " pdb=" CA LEU T2622 " ideal model delta harmonic sigma weight residual 180.00 150.37 29.63 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA THR T2756 " pdb=" C THR T2756 " pdb=" N ASP T2757 " pdb=" CA ASP T2757 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA GLU T2411 " pdb=" C GLU T2411 " pdb=" N ILE T2412 " pdb=" CA ILE T2412 " ideal model delta harmonic sigma weight residual 180.00 151.30 28.70 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 18373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 4401 0.116 - 0.231: 271 0.231 - 0.347: 15 0.347 - 0.463: 0 0.463 - 0.579: 3 Chirality restraints: 4690 Sorted by residual: chirality pdb=" CB ILE T2628 " pdb=" CA ILE T2628 " pdb=" CG1 ILE T2628 " pdb=" CG2 ILE T2628 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.58 2.00e-01 2.50e+01 8.37e+00 chirality pdb=" CB ILE T1848 " pdb=" CA ILE T1848 " pdb=" CG1 ILE T1848 " pdb=" CG2 ILE T1848 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" CG LEU T1021 " pdb=" CB LEU T1021 " pdb=" CD1 LEU T1021 " pdb=" CD2 LEU T1021 " both_signs ideal model delta sigma weight residual False -2.59 -2.08 -0.51 2.00e-01 2.50e+01 6.44e+00 ... (remaining 4687 not shown) Planarity restraints: 5173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR T1348 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" C THR T1348 " -0.063 2.00e-02 2.50e+03 pdb=" O THR T1348 " 0.023 2.00e-02 2.50e+03 pdb=" N MET T1349 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO T2619 " -0.058 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO T2620 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO T2620 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO T2620 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE T2755 " -0.011 2.00e-02 2.50e+03 2.58e-02 1.17e+01 pdb=" CG PHE T2755 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE T2755 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 PHE T2755 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE T2755 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE T2755 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE T2755 " -0.002 2.00e-02 2.50e+03 ... (remaining 5170 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 7171 2.78 - 3.31: 27780 3.31 - 3.84: 48963 3.84 - 4.37: 57486 4.37 - 4.90: 98265 Nonbonded interactions: 239665 Sorted by model distance: nonbonded pdb=" O LEU T1509 " pdb=" OH TYR T1513 " model vdw 2.256 3.040 nonbonded pdb=" O ILE T 467 " pdb=" OG SER T 470 " model vdw 2.265 3.040 nonbonded pdb=" O VAL T1244 " pdb=" OG1 THR T1248 " model vdw 2.284 3.040 nonbonded pdb=" OD1 ASP T 17 " pdb=" OG SER T 26 " model vdw 2.289 3.040 nonbonded pdb=" OE1 GLN T2474 " pdb=" OH TYR T2550 " model vdw 2.289 3.040 ... (remaining 239660 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.190 Check model and map are aligned: 0.240 Set scattering table: 0.280 Process input model: 63.610 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 30193 Z= 0.327 Angle : 1.057 14.260 40913 Z= 0.555 Chirality : 0.062 0.579 4690 Planarity : 0.008 0.087 5173 Dihedral : 15.115 89.768 11312 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.00 % Favored : 91.97 % Rotamer: Outliers : 0.90 % Allowed : 8.50 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.11), residues: 3587 helix: -2.57 (0.08), residues: 2244 sheet: -0.79 (0.67), residues: 54 loop : -3.54 (0.14), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP T2468 HIS 0.012 0.002 HIS T1604 PHE 0.055 0.003 PHE T 317 TYR 0.037 0.002 TYR T3092 ARG 0.010 0.001 ARG T2432 Details of bonding type rmsd hydrogen bonds : bond 0.14361 ( 1474) hydrogen bonds : angle 6.32788 ( 4377) covalent geometry : bond 0.00780 (30193) covalent geometry : angle 1.05683 (40913) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 450 time to evaluate : 3.226 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: symmetry clash revert: symmetry clash REVERT: B 397 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.7840 (mtt) REVERT: I 354 ILE cc_start: 0.8988 (mm) cc_final: 0.8731 (mt) REVERT: T 235 TYR cc_start: 0.7148 (m-10) cc_final: 0.6614 (m-10) REVERT: T 291 TYR cc_start: 0.4802 (OUTLIER) cc_final: 0.4558 (p90) REVERT: T 512 LYS cc_start: 0.8132 (ttpp) cc_final: 0.7486 (mtmm) REVERT: T 1114 GLN cc_start: 0.8495 (tm-30) cc_final: 0.7769 (tm-30) REVERT: T 1251 GLU cc_start: 0.7656 (pm20) cc_final: 0.7406 (pm20) REVERT: T 1379 GLN cc_start: 0.7954 (pp30) cc_final: 0.7732 (pp30) REVERT: T 1486 LEU cc_start: 0.9266 (mm) cc_final: 0.9064 (mm) REVERT: T 1741 ASN cc_start: 0.7968 (p0) cc_final: 0.6625 (p0) REVERT: T 1745 LEU cc_start: 0.9076 (mp) cc_final: 0.8860 (mp) REVERT: T 1799 ARG cc_start: 0.6275 (mmp80) cc_final: 0.5545 (mmp-170) REVERT: T 1971 LYS cc_start: 0.9027 (tppp) cc_final: 0.8799 (tppt) REVERT: T 1988 PHE cc_start: 0.7557 (p90) cc_final: 0.7197 (p90) REVERT: T 1992 HIS cc_start: 0.7319 (m170) cc_final: 0.7059 (m170) REVERT: T 2180 ILE cc_start: 0.8193 (mm) cc_final: 0.7961 (mm) REVERT: T 2181 MET cc_start: 0.7093 (pmm) cc_final: 0.6426 (pmm) REVERT: T 2214 MET cc_start: 0.8244 (tmm) cc_final: 0.7843 (tmm) REVERT: T 2320 LEU cc_start: 0.8573 (tt) cc_final: 0.7573 (tt) REVERT: T 2490 ASN cc_start: 0.6947 (t0) cc_final: 0.6704 (t0) REVERT: T 3506 MET cc_start: 0.7437 (mmp) cc_final: 0.7191 (mmt) outliers start: 30 outliers final: 12 residues processed: 475 average time/residue: 0.4873 time to fit residues: 353.2399 Evaluate side-chains 346 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 332 time to evaluate : 3.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain I residue 382 ARG Chi-restraints excluded: chain T residue 291 TYR Chi-restraints excluded: chain T residue 295 ILE Chi-restraints excluded: chain T residue 296 LEU Chi-restraints excluded: chain T residue 300 LYS Chi-restraints excluded: chain T residue 907 ASN Chi-restraints excluded: chain T residue 908 LEU Chi-restraints excluded: chain T residue 1021 LEU Chi-restraints excluded: chain T residue 1775 ASN Chi-restraints excluded: chain T residue 1849 LEU Chi-restraints excluded: chain T residue 1852 ASP Chi-restraints excluded: chain T residue 2272 VAL Chi-restraints excluded: chain T residue 2276 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 1.9990 chunk 273 optimal weight: 0.9990 chunk 151 optimal weight: 0.4980 chunk 93 optimal weight: 0.8980 chunk 184 optimal weight: 0.0000 chunk 146 optimal weight: 2.9990 chunk 282 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 210 optimal weight: 9.9990 chunk 327 optimal weight: 0.7980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN I 357 GLN T 49 GLN T 77 ASN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 114 ASN T 150 ASN T 153 ASN T 379 ASN T 441 ASN T 510 ASN T 565 ASN T 639 HIS T 699 ASN T 735 ASN T 794 ASN T 840 GLN T 843 ASN T 938 ASN T 939 HIS T1105 ASN T1109 HIS T1298 ASN T1479 GLN T1546 GLN T1565 GLN T1587 GLN T1619 GLN T1626 ASN T1629 GLN T1654 ASN T1659 GLN T1719 ASN ** T1844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T1856 HIS T1857 HIS ** T1892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T1903 GLN T1958 ASN T1968 ASN ** T2266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2354 ASN T2441 ASN T2474 GLN T2521 ASN T2557 HIS ** T2621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2644 GLN T2668 ASN T2770 ASN T2811 GLN T2822 GLN T2863 HIS T2906 GLN T2910 GLN T2952 HIS T2992 HIS T3040 ASN T3064 ASN T3250 ASN T3259 ASN T3261 ASN T3340 HIS T3357 GLN T3433 ASN T3442 GLN ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3486 GLN T3537 GLN T3570 HIS Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.135699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.094860 restraints weight = 54165.275| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.19 r_work: 0.3047 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30193 Z= 0.136 Angle : 0.657 14.344 40913 Z= 0.334 Chirality : 0.042 0.196 4690 Planarity : 0.005 0.067 5173 Dihedral : 6.050 56.296 3932 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.66 % Favored : 93.31 % Rotamer: Outliers : 1.35 % Allowed : 12.79 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.13), residues: 3587 helix: -0.77 (0.10), residues: 2246 sheet: -0.64 (0.68), residues: 54 loop : -3.23 (0.15), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP T3205 HIS 0.012 0.001 HIS T2621 PHE 0.029 0.001 PHE T 309 TYR 0.020 0.001 TYR T 321 ARG 0.006 0.000 ARG T1531 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 1474) hydrogen bonds : angle 4.34305 ( 4377) covalent geometry : bond 0.00299 (30193) covalent geometry : angle 0.65676 (40913) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 373 time to evaluate : 3.221 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: I 354 ILE cc_start: 0.9186 (mm) cc_final: 0.8970 (mt) REVERT: T 1 MET cc_start: 0.4137 (tpp) cc_final: 0.3921 (tpt) REVERT: T 93 GLN cc_start: 0.9385 (mm-40) cc_final: 0.9030 (mm-40) REVERT: T 97 MET cc_start: 0.8862 (mmm) cc_final: 0.8510 (mmm) REVERT: T 120 LYS cc_start: 0.7987 (mmmt) cc_final: 0.7731 (mmmt) REVERT: T 148 TYR cc_start: 0.9445 (m-80) cc_final: 0.9029 (m-80) REVERT: T 214 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8305 (tt) REVERT: T 235 TYR cc_start: 0.7802 (m-10) cc_final: 0.7136 (m-80) REVERT: T 250 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7258 (p) REVERT: T 300 LYS cc_start: 0.9435 (mmmt) cc_final: 0.9233 (tptp) REVERT: T 903 LEU cc_start: 0.8508 (tp) cc_final: 0.8186 (tp) REVERT: T 1054 ARG cc_start: 0.7654 (tpp-160) cc_final: 0.7307 (mmp-170) REVERT: T 1114 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8185 (tm-30) REVERT: T 1251 GLU cc_start: 0.8058 (pm20) cc_final: 0.7788 (pm20) REVERT: T 1376 ARG cc_start: 0.8610 (ttm110) cc_final: 0.8302 (tpp80) REVERT: T 1676 MET cc_start: 0.8697 (mmp) cc_final: 0.8321 (mmm) REVERT: T 1741 ASN cc_start: 0.8168 (p0) cc_final: 0.7792 (p0) REVERT: T 1799 ARG cc_start: 0.6104 (mmp80) cc_final: 0.5223 (mmp-170) REVERT: T 2214 MET cc_start: 0.8514 (tmm) cc_final: 0.8222 (tmm) REVERT: T 2239 LEU cc_start: 0.9375 (tt) cc_final: 0.8825 (mt) REVERT: T 2490 ASN cc_start: 0.7133 (t0) cc_final: 0.6861 (t0) REVERT: T 3029 PHE cc_start: 0.8414 (m-80) cc_final: 0.8093 (m-80) REVERT: T 3154 HIS cc_start: 0.8428 (OUTLIER) cc_final: 0.8142 (t-90) REVERT: T 3254 ILE cc_start: 0.9053 (pt) cc_final: 0.8737 (mt) REVERT: T 3506 MET cc_start: 0.7582 (mmp) cc_final: 0.7296 (mmt) outliers start: 45 outliers final: 29 residues processed: 406 average time/residue: 0.4285 time to fit residues: 280.8547 Evaluate side-chains 356 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 324 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 385 ILE Chi-restraints excluded: chain I residue 389 SER Chi-restraints excluded: chain T residue 214 LEU Chi-restraints excluded: chain T residue 250 THR Chi-restraints excluded: chain T residue 296 LEU Chi-restraints excluded: chain T residue 304 PHE Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain T residue 376 LEU Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain T residue 907 ASN Chi-restraints excluded: chain T residue 989 VAL Chi-restraints excluded: chain T residue 1021 LEU Chi-restraints excluded: chain T residue 1160 VAL Chi-restraints excluded: chain T residue 1275 VAL Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1482 LEU Chi-restraints excluded: chain T residue 1768 HIS Chi-restraints excluded: chain T residue 2272 VAL Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2414 VAL Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2651 ASN Chi-restraints excluded: chain T residue 2760 LEU Chi-restraints excluded: chain T residue 2866 THR Chi-restraints excluded: chain T residue 2973 LEU Chi-restraints excluded: chain T residue 3108 ILE Chi-restraints excluded: chain T residue 3154 HIS Chi-restraints excluded: chain T residue 3178 PHE Chi-restraints excluded: chain T residue 3360 LEU Chi-restraints excluded: chain T residue 3371 ILE Chi-restraints excluded: chain T residue 3596 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 254 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 chunk 339 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 308 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 227 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 314 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN T 58 GLN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 935 GLN T1002 ASN T1199 HIS T1298 ASN T1350 GLN T1365 ASN T1480 ASN T1781 ASN ** T1844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T1944 GLN T2188 GLN T2704 GLN T2913 ASN T2948 ASN T3139 GLN T3250 ASN T3261 ASN T3367 HIS ** T3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.131904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.102800 restraints weight = 55167.743| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.90 r_work: 0.3022 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 30193 Z= 0.336 Angle : 0.796 11.303 40913 Z= 0.405 Chirality : 0.051 0.429 4690 Planarity : 0.006 0.104 5173 Dihedral : 6.135 59.417 3909 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 2.85 % Allowed : 14.86 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.14), residues: 3587 helix: -0.28 (0.11), residues: 2262 sheet: -0.53 (0.78), residues: 49 loop : -3.09 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP T1842 HIS 0.008 0.002 HIS T3345 PHE 0.031 0.002 PHE T2755 TYR 0.038 0.002 TYR T2630 ARG 0.006 0.001 ARG T 855 Details of bonding type rmsd hydrogen bonds : bond 0.05230 ( 1474) hydrogen bonds : angle 4.42000 ( 4377) covalent geometry : bond 0.00800 (30193) covalent geometry : angle 0.79603 (40913) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 335 time to evaluate : 3.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 354 ILE cc_start: 0.9267 (mm) cc_final: 0.8954 (mt) REVERT: T 1 MET cc_start: 0.3812 (tpp) cc_final: 0.3477 (tpp) REVERT: T 3 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7563 (mm) REVERT: T 35 MET cc_start: 0.6332 (mmm) cc_final: 0.6063 (mmm) REVERT: T 456 GLU cc_start: 0.6647 (pp20) cc_final: 0.6445 (pp20) REVERT: T 960 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.7671 (mt) REVERT: T 1114 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8508 (tm-30) REVERT: T 1125 TYR cc_start: 0.6401 (t80) cc_final: 0.6173 (t80) REVERT: T 1251 GLU cc_start: 0.8009 (pm20) cc_final: 0.7746 (pm20) REVERT: T 1376 ARG cc_start: 0.8491 (ttm110) cc_final: 0.8247 (ttm-80) REVERT: T 1426 GLU cc_start: 0.8417 (tp30) cc_final: 0.7726 (tp30) REVERT: T 1592 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.7721 (p90) REVERT: T 1676 MET cc_start: 0.8698 (mmp) cc_final: 0.8405 (mmm) REVERT: T 1741 ASN cc_start: 0.7987 (p0) cc_final: 0.7079 (p0) REVERT: T 1745 LEU cc_start: 0.9110 (mp) cc_final: 0.8852 (mp) REVERT: T 1799 ARG cc_start: 0.6392 (mmp80) cc_final: 0.5803 (mmp-170) REVERT: T 1988 PHE cc_start: 0.7996 (p90) cc_final: 0.7389 (p90) REVERT: T 2214 MET cc_start: 0.8567 (tmm) cc_final: 0.8207 (tmm) REVERT: T 2490 ASN cc_start: 0.7100 (t0) cc_final: 0.6783 (t0) REVERT: T 2608 ASP cc_start: 0.8452 (t0) cc_final: 0.8170 (t0) REVERT: T 3029 PHE cc_start: 0.8249 (m-80) cc_final: 0.8025 (m-80) REVERT: T 3313 ARG cc_start: 0.7833 (ptt90) cc_final: 0.7200 (tmt170) REVERT: T 3506 MET cc_start: 0.7727 (mmp) cc_final: 0.7412 (mmt) outliers start: 95 outliers final: 60 residues processed: 407 average time/residue: 0.4088 time to fit residues: 272.9050 Evaluate side-chains 376 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 313 time to evaluate : 3.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain I residue 385 ILE Chi-restraints excluded: chain I residue 389 SER Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain T residue 376 LEU Chi-restraints excluded: chain T residue 387 LEU Chi-restraints excluded: chain T residue 443 VAL Chi-restraints excluded: chain T residue 570 LEU Chi-restraints excluded: chain T residue 574 THR Chi-restraints excluded: chain T residue 697 THR Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain T residue 803 GLU Chi-restraints excluded: chain T residue 807 VAL Chi-restraints excluded: chain T residue 871 VAL Chi-restraints excluded: chain T residue 907 ASN Chi-restraints excluded: chain T residue 960 LEU Chi-restraints excluded: chain T residue 989 VAL Chi-restraints excluded: chain T residue 1021 LEU Chi-restraints excluded: chain T residue 1160 VAL Chi-restraints excluded: chain T residue 1275 VAL Chi-restraints excluded: chain T residue 1298 ASN Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1400 THR Chi-restraints excluded: chain T residue 1489 LEU Chi-restraints excluded: chain T residue 1510 LEU Chi-restraints excluded: chain T residue 1592 PHE Chi-restraints excluded: chain T residue 1768 HIS Chi-restraints excluded: chain T residue 1788 LEU Chi-restraints excluded: chain T residue 1800 ILE Chi-restraints excluded: chain T residue 1803 LEU Chi-restraints excluded: chain T residue 1806 VAL Chi-restraints excluded: chain T residue 1899 THR Chi-restraints excluded: chain T residue 1911 TYR Chi-restraints excluded: chain T residue 1986 TYR Chi-restraints excluded: chain T residue 2143 PHE Chi-restraints excluded: chain T residue 2237 GLN Chi-restraints excluded: chain T residue 2272 VAL Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2317 ILE Chi-restraints excluded: chain T residue 2339 LEU Chi-restraints excluded: chain T residue 2377 THR Chi-restraints excluded: chain T residue 2414 VAL Chi-restraints excluded: chain T residue 2504 LEU Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2616 LEU Chi-restraints excluded: chain T residue 2760 LEU Chi-restraints excluded: chain T residue 2866 THR Chi-restraints excluded: chain T residue 2895 VAL Chi-restraints excluded: chain T residue 2973 LEU Chi-restraints excluded: chain T residue 3108 ILE Chi-restraints excluded: chain T residue 3173 THR Chi-restraints excluded: chain T residue 3178 PHE Chi-restraints excluded: chain T residue 3288 LEU Chi-restraints excluded: chain T residue 3307 TYR Chi-restraints excluded: chain T residue 3360 LEU Chi-restraints excluded: chain T residue 3371 ILE Chi-restraints excluded: chain T residue 3400 VAL Chi-restraints excluded: chain T residue 3419 MET Chi-restraints excluded: chain T residue 3564 ILE Chi-restraints excluded: chain T residue 3596 VAL Chi-restraints excluded: chain T residue 3658 GLU Chi-restraints excluded: chain T residue 3724 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 274 optimal weight: 0.6980 chunk 350 optimal weight: 0.6980 chunk 281 optimal weight: 0.5980 chunk 192 optimal weight: 6.9990 chunk 333 optimal weight: 0.9990 chunk 254 optimal weight: 0.0570 chunk 78 optimal weight: 0.9990 chunk 322 optimal weight: 0.9980 chunk 292 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN T 615 ASN T 840 GLN ** T1844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3261 ASN ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3486 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.135639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.106436 restraints weight = 55113.327| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.02 r_work: 0.3101 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30193 Z= 0.126 Angle : 0.648 13.638 40913 Z= 0.324 Chirality : 0.043 0.196 4690 Planarity : 0.004 0.055 5173 Dihedral : 5.577 54.870 3907 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.89 % Favored : 93.09 % Rotamer: Outliers : 2.43 % Allowed : 16.48 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3587 helix: 0.26 (0.11), residues: 2241 sheet: -0.75 (0.71), residues: 54 loop : -2.87 (0.16), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP T1842 HIS 0.006 0.001 HIS T1604 PHE 0.024 0.001 PHE T2099 TYR 0.025 0.001 TYR T 828 ARG 0.004 0.000 ARG T 855 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 1474) hydrogen bonds : angle 4.04980 ( 4377) covalent geometry : bond 0.00278 (30193) covalent geometry : angle 0.64766 (40913) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 343 time to evaluate : 3.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 354 ILE cc_start: 0.9229 (mm) cc_final: 0.8950 (mt) REVERT: T 1 MET cc_start: 0.3567 (tpp) cc_final: 0.3203 (tpp) REVERT: T 3 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7544 (mm) REVERT: T 235 TYR cc_start: 0.7372 (m-10) cc_final: 0.6963 (m-80) REVERT: T 960 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7399 (mt) REVERT: T 1114 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8115 (tm-30) REVERT: T 1156 TYR cc_start: 0.8352 (p90) cc_final: 0.7794 (p90) REVERT: T 1251 GLU cc_start: 0.7813 (pm20) cc_final: 0.7610 (pm20) REVERT: T 1376 ARG cc_start: 0.8410 (ttm110) cc_final: 0.8179 (ttm-80) REVERT: T 1676 MET cc_start: 0.8590 (mmp) cc_final: 0.8205 (mmm) REVERT: T 1741 ASN cc_start: 0.8033 (p0) cc_final: 0.7167 (p0) REVERT: T 1799 ARG cc_start: 0.5981 (mmp80) cc_final: 0.5665 (mmp-170) REVERT: T 2214 MET cc_start: 0.8454 (tmm) cc_final: 0.8242 (tmm) REVERT: T 2299 MET cc_start: 0.6233 (pmm) cc_final: 0.5631 (mmp) REVERT: T 2490 ASN cc_start: 0.7184 (t0) cc_final: 0.6872 (t0) REVERT: T 3313 ARG cc_start: 0.7660 (ptt90) cc_final: 0.6944 (tmt170) outliers start: 81 outliers final: 52 residues processed: 403 average time/residue: 0.4268 time to fit residues: 279.6416 Evaluate side-chains 368 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 314 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain I residue 389 SER Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain T residue 281 ILE Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain T residue 376 LEU Chi-restraints excluded: chain T residue 443 VAL Chi-restraints excluded: chain T residue 615 ASN Chi-restraints excluded: chain T residue 697 THR Chi-restraints excluded: chain T residue 720 LEU Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain T residue 803 GLU Chi-restraints excluded: chain T residue 907 ASN Chi-restraints excluded: chain T residue 917 ILE Chi-restraints excluded: chain T residue 960 LEU Chi-restraints excluded: chain T residue 989 VAL Chi-restraints excluded: chain T residue 1021 LEU Chi-restraints excluded: chain T residue 1275 VAL Chi-restraints excluded: chain T residue 1392 LEU Chi-restraints excluded: chain T residue 1482 LEU Chi-restraints excluded: chain T residue 1534 VAL Chi-restraints excluded: chain T residue 1568 MET Chi-restraints excluded: chain T residue 1569 PHE Chi-restraints excluded: chain T residue 1768 HIS Chi-restraints excluded: chain T residue 1788 LEU Chi-restraints excluded: chain T residue 1803 LEU Chi-restraints excluded: chain T residue 1899 THR Chi-restraints excluded: chain T residue 1911 TYR Chi-restraints excluded: chain T residue 1950 THR Chi-restraints excluded: chain T residue 1986 TYR Chi-restraints excluded: chain T residue 2143 PHE Chi-restraints excluded: chain T residue 2237 GLN Chi-restraints excluded: chain T residue 2272 VAL Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2414 VAL Chi-restraints excluded: chain T residue 2504 LEU Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2616 LEU Chi-restraints excluded: chain T residue 2618 LEU Chi-restraints excluded: chain T residue 2651 ASN Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2760 LEU Chi-restraints excluded: chain T residue 2866 THR Chi-restraints excluded: chain T residue 2973 LEU Chi-restraints excluded: chain T residue 3154 HIS Chi-restraints excluded: chain T residue 3178 PHE Chi-restraints excluded: chain T residue 3288 LEU Chi-restraints excluded: chain T residue 3307 TYR Chi-restraints excluded: chain T residue 3360 LEU Chi-restraints excluded: chain T residue 3371 ILE Chi-restraints excluded: chain T residue 3480 PHE Chi-restraints excluded: chain T residue 3596 VAL Chi-restraints excluded: chain T residue 3678 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 338 optimal weight: 2.9990 chunk 237 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 309 optimal weight: 5.9990 chunk 129 optimal weight: 0.0670 chunk 360 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 186 optimal weight: 0.0060 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN T 84 ASN T 93 GLN T 840 GLN T 843 ASN T1298 ASN T1492 HIS ** T1844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3261 ASN T3472 ASN T3497 HIS T3705 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.135302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.102683 restraints weight = 54125.240| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.93 r_work: 0.3019 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30193 Z= 0.120 Angle : 0.628 12.538 40913 Z= 0.313 Chirality : 0.042 0.180 4690 Planarity : 0.004 0.058 5173 Dihedral : 5.336 58.116 3907 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.52 % Allowed : 17.62 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3587 helix: 0.56 (0.11), residues: 2238 sheet: -0.74 (0.71), residues: 54 loop : -2.78 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP T1842 HIS 0.006 0.001 HIS T1604 PHE 0.029 0.001 PHE T2099 TYR 0.029 0.001 TYR T 828 ARG 0.004 0.000 ARG T1731 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 1474) hydrogen bonds : angle 3.91393 ( 4377) covalent geometry : bond 0.00263 (30193) covalent geometry : angle 0.62758 (40913) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 339 time to evaluate : 3.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 354 ILE cc_start: 0.9227 (mm) cc_final: 0.8954 (mt) REVERT: I 389 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8423 (p) REVERT: I 409 MET cc_start: 0.5197 (mmt) cc_final: 0.4035 (ttp) REVERT: T 3 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7839 (mm) REVERT: T 235 TYR cc_start: 0.7847 (m-10) cc_final: 0.7445 (m-80) REVERT: T 1021 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8718 (mt) REVERT: T 1114 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8600 (tm-30) REVERT: T 1156 TYR cc_start: 0.8465 (p90) cc_final: 0.7834 (p90) REVERT: T 1251 GLU cc_start: 0.7800 (pm20) cc_final: 0.7539 (pm20) REVERT: T 1376 ARG cc_start: 0.8589 (ttm110) cc_final: 0.8382 (ttm-80) REVERT: T 1501 ASP cc_start: 0.7963 (t0) cc_final: 0.7420 (t0) REVERT: T 1676 MET cc_start: 0.8701 (mmp) cc_final: 0.8257 (mmm) REVERT: T 1799 ARG cc_start: 0.5969 (mmp80) cc_final: 0.5653 (mmp-170) REVERT: T 1861 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8343 (mtt-85) REVERT: T 2214 MET cc_start: 0.8734 (tmm) cc_final: 0.8158 (tmm) REVERT: T 2239 LEU cc_start: 0.9112 (tt) cc_final: 0.8630 (mt) REVERT: T 2299 MET cc_start: 0.6648 (pmm) cc_final: 0.6016 (mmp) REVERT: T 2490 ASN cc_start: 0.6923 (t0) cc_final: 0.6716 (t0) REVERT: T 2628 ILE cc_start: 0.6684 (OUTLIER) cc_final: 0.6042 (pt) REVERT: T 3022 PHE cc_start: 0.6641 (m-10) cc_final: 0.6381 (m-10) REVERT: T 3266 PRO cc_start: 0.5373 (Cg_exo) cc_final: 0.5100 (Cg_endo) REVERT: T 3313 ARG cc_start: 0.7688 (ptt90) cc_final: 0.7067 (tmt170) REVERT: T 3349 PHE cc_start: 0.8259 (p90) cc_final: 0.7980 (p90) outliers start: 84 outliers final: 54 residues processed: 403 average time/residue: 0.4375 time to fit residues: 287.1598 Evaluate side-chains 369 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 310 time to evaluate : 3.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain I residue 385 ILE Chi-restraints excluded: chain I residue 389 SER Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain T residue 93 GLN Chi-restraints excluded: chain T residue 281 ILE Chi-restraints excluded: chain T residue 304 PHE Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain T residue 376 LEU Chi-restraints excluded: chain T residue 387 LEU Chi-restraints excluded: chain T residue 574 THR Chi-restraints excluded: chain T residue 619 TRP Chi-restraints excluded: chain T residue 697 THR Chi-restraints excluded: chain T residue 703 GLU Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain T residue 803 GLU Chi-restraints excluded: chain T residue 917 ILE Chi-restraints excluded: chain T residue 1021 LEU Chi-restraints excluded: chain T residue 1275 VAL Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1392 LEU Chi-restraints excluded: chain T residue 1482 LEU Chi-restraints excluded: chain T residue 1534 VAL Chi-restraints excluded: chain T residue 1768 HIS Chi-restraints excluded: chain T residue 1788 LEU Chi-restraints excluded: chain T residue 1803 LEU Chi-restraints excluded: chain T residue 1860 PHE Chi-restraints excluded: chain T residue 1861 ARG Chi-restraints excluded: chain T residue 1899 THR Chi-restraints excluded: chain T residue 1911 TYR Chi-restraints excluded: chain T residue 1950 THR Chi-restraints excluded: chain T residue 2124 LEU Chi-restraints excluded: chain T residue 2143 PHE Chi-restraints excluded: chain T residue 2237 GLN Chi-restraints excluded: chain T residue 2272 VAL Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2315 LEU Chi-restraints excluded: chain T residue 2317 ILE Chi-restraints excluded: chain T residue 2414 VAL Chi-restraints excluded: chain T residue 2504 LEU Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2616 LEU Chi-restraints excluded: chain T residue 2628 ILE Chi-restraints excluded: chain T residue 2651 ASN Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2760 LEU Chi-restraints excluded: chain T residue 2866 THR Chi-restraints excluded: chain T residue 2973 LEU Chi-restraints excluded: chain T residue 3001 THR Chi-restraints excluded: chain T residue 3154 HIS Chi-restraints excluded: chain T residue 3178 PHE Chi-restraints excluded: chain T residue 3307 TYR Chi-restraints excluded: chain T residue 3332 GLU Chi-restraints excluded: chain T residue 3360 LEU Chi-restraints excluded: chain T residue 3371 ILE Chi-restraints excluded: chain T residue 3449 ILE Chi-restraints excluded: chain T residue 3596 VAL Chi-restraints excluded: chain T residue 3678 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.2174 > 50: distance: 26 - 49: 37.600 distance: 31 - 57: 31.390 distance: 46 - 49: 34.611 distance: 49 - 50: 56.612 distance: 50 - 51: 39.246 distance: 50 - 53: 40.523 distance: 51 - 57: 40.816 distance: 53 - 54: 38.611 distance: 54 - 55: 70.122 distance: 54 - 56: 55.499 distance: 57 - 58: 40.427 distance: 58 - 59: 69.722 distance: 58 - 61: 38.788 distance: 59 - 60: 39.937 distance: 59 - 65: 39.750 distance: 61 - 62: 40.944 distance: 62 - 63: 38.614 distance: 62 - 64: 67.807 distance: 65 - 66: 39.371 distance: 66 - 67: 56.467 distance: 66 - 69: 43.419 distance: 67 - 68: 39.202 distance: 67 - 76: 41.351 distance: 69 - 70: 46.197 distance: 70 - 71: 68.253 distance: 72 - 73: 39.974 distance: 73 - 74: 57.353 distance: 73 - 75: 56.045 distance: 76 - 77: 39.369 distance: 77 - 78: 56.256 distance: 77 - 80: 38.809 distance: 78 - 79: 39.615 distance: 80 - 81: 69.434 distance: 82 - 83: 56.330 distance: 83 - 84: 39.285 distance: 83 - 86: 69.071 distance: 84 - 85: 39.426 distance: 86 - 87: 39.625 distance: 88 - 89: 56.486 distance: 89 - 90: 39.828 distance: 90 - 91: 40.548 distance: 90 - 98: 68.503 distance: 92 - 93: 39.841 distance: 93 - 94: 69.757 distance: 93 - 95: 56.782 distance: 94 - 96: 68.115 distance: 95 - 97: 68.449 distance: 96 - 97: 41.192 distance: 98 - 99: 40.240 distance: 99 - 100: 56.773 distance: 99 - 102: 38.537 distance: 100 - 101: 39.725 distance: 100 - 105: 40.661 distance: 102 - 103: 55.702 distance: 102 - 104: 38.966 distance: 105 - 106: 55.892 distance: 106 - 107: 41.380 distance: 106 - 109: 40.288 distance: 107 - 108: 38.903 distance: 109 - 110: 40.178 distance: 110 - 111: 56.654 distance: 111 - 112: 56.879 distance: 111 - 113: 56.173 distance: 115 - 116: 68.229 distance: 115 - 118: 40.064 distance: 119 - 120: 38.791 distance: 120 - 121: 40.611 distance: 120 - 123: 69.440 distance: 121 - 122: 39.534 distance: 121 - 130: 34.017 distance: 122 - 149: 35.804 distance: 123 - 124: 55.939 distance: 124 - 125: 40.062 distance: 125 - 126: 57.133 distance: 127 - 128: 39.532