Starting phenix.real_space_refine on Thu Jan 15 10:19:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u8a_42019/01_2026/8u8a_42019.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u8a_42019/01_2026/8u8a_42019.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/8u8a_42019/01_2026/8u8a_42019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u8a_42019/01_2026/8u8a_42019.map" model { file = "/net/cci-nas-00/data/ceres_data/8u8a_42019/01_2026/8u8a_42019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u8a_42019/01_2026/8u8a_42019.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.065 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 P 4 5.49 5 S 144 5.16 5 C 15742 2.51 5 N 4182 2.21 5 O 4350 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24428 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 12147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1705, 12147 Classifications: {'peptide': 1705} Incomplete info: {'truncation_to_alanine': 366} Link IDs: {'PCIS': 2, 'PTRANS': 71, 'TRANS': 1631} Chain breaks: 15 Unresolved non-hydrogen bonds: 1422 Unresolved non-hydrogen angles: 1738 Unresolved non-hydrogen dihedrals: 1165 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'ASP:plan': 49, 'HIS:plan': 13, 'GLN:plan1': 33, 'TYR:plan': 4, 'GLU:plan': 71, 'ARG:plan': 30, 'PHE:plan': 7, 'ASN:plan1': 23, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 926 Chain: "C" Number of atoms: 12147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1705, 12147 Classifications: {'peptide': 1705} Incomplete info: {'truncation_to_alanine': 366} Link IDs: {'PCIS': 2, 'PTRANS': 71, 'TRANS': 1631} Chain breaks: 15 Unresolved non-hydrogen bonds: 1422 Unresolved non-hydrogen angles: 1738 Unresolved non-hydrogen dihedrals: 1165 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'ASP:plan': 49, 'HIS:plan': 13, 'GLN:plan1': 33, 'TYR:plan': 4, 'GLU:plan': 71, 'ARG:plan': 30, 'PHE:plan': 7, 'ASN:plan1': 23, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 926 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'0LI': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'0LI': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.10, per 1000 atoms: 0.21 Number of scatterers: 24428 At special positions: 0 Unit cell: (177.689, 138.779, 149.155, 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) S 144 16.00 P 4 15.00 F 6 9.00 O 4350 8.00 N 4182 7.00 C 15742 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: 2.11 Conformation dependent library (CDL) restraints added in 1.1 seconds 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6508 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 32 sheets defined 36.8% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'B' and resid 559 through 571 Processing helix chain 'B' and resid 585 through 596 Processing helix chain 'B' and resid 598 through 603 removed outlier: 3.682A pdb=" N GLN B 603 " --> pdb=" O ASP B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 607 Processing helix chain 'B' and resid 624 through 639 removed outlier: 3.895A pdb=" N ALA B 628 " --> pdb=" O GLY B 624 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE B 638 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 659 removed outlier: 3.549A pdb=" N THR B 646 " --> pdb=" O ALA B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 670 removed outlier: 4.123A pdb=" N LYS B 664 " --> pdb=" O ALA B 660 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 665 " --> pdb=" O SER B 661 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 670 " --> pdb=" O LEU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 681 removed outlier: 3.597A pdb=" N VAL B 674 " --> pdb=" O SER B 670 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N HIS B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 703 Processing helix chain 'B' and resid 705 through 719 removed outlier: 3.889A pdb=" N LYS B 709 " --> pdb=" O ASP B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 732 removed outlier: 3.778A pdb=" N VAL B 725 " --> pdb=" O ASN B 721 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU B 726 " --> pdb=" O SER B 722 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N CYS B 727 " --> pdb=" O ILE B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 754 through 764 Processing helix chain 'B' and resid 767 through 781 Processing helix chain 'B' and resid 783 through 795 removed outlier: 3.927A pdb=" N ARG B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 819 removed outlier: 3.577A pdb=" N LEU B 818 " --> pdb=" O GLU B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 853 Processing helix chain 'B' and resid 1006 through 1011 removed outlier: 3.598A pdb=" N GLU B1011 " --> pdb=" O SER B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1034 Processing helix chain 'B' and resid 1051 through 1057 Processing helix chain 'B' and resid 1101 through 1106 Processing helix chain 'B' and resid 1240 through 1245 removed outlier: 3.584A pdb=" N TRP B1244 " --> pdb=" O ALA B1241 " (cutoff:3.500A) Processing helix chain 'B' and resid 1261 through 1267 removed outlier: 4.015A pdb=" N GLY B1265 " --> pdb=" O PRO B1262 " (cutoff:3.500A) Processing helix chain 'B' and resid 1285 through 1291 Processing helix chain 'B' and resid 1314 through 1328 removed outlier: 3.814A pdb=" N LYS B1327 " --> pdb=" O GLN B1323 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B1328 " --> pdb=" O GLN B1324 " (cutoff:3.500A) Processing helix chain 'B' and resid 1347 through 1355 Processing helix chain 'B' and resid 1398 through 1402 removed outlier: 3.630A pdb=" N PHE B1401 " --> pdb=" O ARG B1398 " (cutoff:3.500A) Processing helix chain 'B' and resid 1404 through 1409 removed outlier: 4.040A pdb=" N MET B1409 " --> pdb=" O PRO B1406 " (cutoff:3.500A) Processing helix chain 'B' and resid 1420 through 1424 Processing helix chain 'B' and resid 1431 through 1442 Processing helix chain 'B' and resid 1463 through 1465 No H-bonds generated for 'chain 'B' and resid 1463 through 1465' Processing helix chain 'B' and resid 1466 through 1473 Processing helix chain 'B' and resid 1494 through 1510 Processing helix chain 'B' and resid 1517 through 1520 Processing helix chain 'B' and resid 1525 through 1538 Processing helix chain 'B' and resid 1550 through 1560 Processing helix chain 'B' and resid 1568 through 1579 Processing helix chain 'B' and resid 1599 through 1608 removed outlier: 4.040A pdb=" N LEU B1603 " --> pdb=" O GLU B1599 " (cutoff:3.500A) Processing helix chain 'B' and resid 1609 through 1613 Processing helix chain 'B' and resid 1645 through 1656 Processing helix chain 'B' and resid 1703 through 1712 Processing helix chain 'B' and resid 1770 through 1792 Processing helix chain 'B' and resid 1793 through 1796 Processing helix chain 'B' and resid 1829 through 1835 Processing helix chain 'B' and resid 1853 through 1855 No H-bonds generated for 'chain 'B' and resid 1853 through 1855' Processing helix chain 'B' and resid 1881 through 1885 Processing helix chain 'B' and resid 1914 through 1926 removed outlier: 4.082A pdb=" N HIS B1926 " --> pdb=" O VAL B1922 " (cutoff:3.500A) Processing helix chain 'B' and resid 1954 through 1961 removed outlier: 3.706A pdb=" N LEU B1958 " --> pdb=" O SER B1954 " (cutoff:3.500A) Processing helix chain 'B' and resid 1962 through 1966 Processing helix chain 'B' and resid 1967 through 1988 Processing helix chain 'B' and resid 1996 through 1998 No H-bonds generated for 'chain 'B' and resid 1996 through 1998' Processing helix chain 'B' and resid 2040 through 2045 Processing helix chain 'B' and resid 2051 through 2068 removed outlier: 3.852A pdb=" N ASP B2055 " --> pdb=" O ASN B2051 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B2056 " --> pdb=" O GLN B2052 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR B2057 " --> pdb=" O GLN B2053 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2099 Processing helix chain 'B' and resid 2104 through 2115 Processing helix chain 'B' and resid 2118 through 2122 Processing helix chain 'B' and resid 2124 through 2132 Processing helix chain 'B' and resid 2134 through 2139 removed outlier: 3.670A pdb=" N VAL B2138 " --> pdb=" O SER B2134 " (cutoff:3.500A) Processing helix chain 'B' and resid 2278 through 2282 removed outlier: 3.720A pdb=" N LEU B2282 " --> pdb=" O THR B2279 " (cutoff:3.500A) Processing helix chain 'B' and resid 2308 through 2312 Processing helix chain 'B' and resid 2339 through 2344 removed outlier: 3.732A pdb=" N GLN B2342 " --> pdb=" O ARG B2339 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2351 Processing helix chain 'B' and resid 2389 through 2395 Processing helix chain 'B' and resid 2499 through 2526 Processing helix chain 'C' and resid 559 through 571 Processing helix chain 'C' and resid 585 through 596 Processing helix chain 'C' and resid 598 through 603 removed outlier: 3.647A pdb=" N GLN C 603 " --> pdb=" O ASP C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 607 Processing helix chain 'C' and resid 624 through 639 removed outlier: 3.868A pdb=" N ALA C 628 " --> pdb=" O GLY C 624 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE C 638 " --> pdb=" O SER C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 659 removed outlier: 3.551A pdb=" N THR C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 670 removed outlier: 4.073A pdb=" N LYS C 664 " --> pdb=" O ALA C 660 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 665 " --> pdb=" O SER C 661 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER C 670 " --> pdb=" O LEU C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 681 removed outlier: 3.591A pdb=" N VAL C 674 " --> pdb=" O SER C 670 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N HIS C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 703 Processing helix chain 'C' and resid 706 through 719 Processing helix chain 'C' and resid 721 through 733 removed outlier: 3.737A pdb=" N VAL C 725 " --> pdb=" O ASN C 721 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU C 726 " --> pdb=" O SER C 722 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N CYS C 727 " --> pdb=" O ILE C 723 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA C 733 " --> pdb=" O LEU C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 751 removed outlier: 3.503A pdb=" N LYS C 751 " --> pdb=" O GLN C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 764 Processing helix chain 'C' and resid 767 through 781 Processing helix chain 'C' and resid 783 through 795 removed outlier: 3.926A pdb=" N ARG C 793 " --> pdb=" O LEU C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 819 removed outlier: 3.579A pdb=" N LEU C 818 " --> pdb=" O GLU C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 853 Processing helix chain 'C' and resid 1006 through 1011 removed outlier: 3.603A pdb=" N GLU C1011 " --> pdb=" O SER C1007 " (cutoff:3.500A) Processing helix chain 'C' and resid 1027 through 1034 Processing helix chain 'C' and resid 1051 through 1057 Processing helix chain 'C' and resid 1101 through 1106 Processing helix chain 'C' and resid 1240 through 1245 removed outlier: 3.582A pdb=" N TRP C1244 " --> pdb=" O ALA C1241 " (cutoff:3.500A) Processing helix chain 'C' and resid 1261 through 1267 removed outlier: 4.012A pdb=" N GLY C1265 " --> pdb=" O PRO C1262 " (cutoff:3.500A) Processing helix chain 'C' and resid 1285 through 1291 Processing helix chain 'C' and resid 1314 through 1328 removed outlier: 3.855A pdb=" N LYS C1327 " --> pdb=" O GLN C1323 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C1328 " --> pdb=" O GLN C1324 " (cutoff:3.500A) Processing helix chain 'C' and resid 1347 through 1355 Processing helix chain 'C' and resid 1398 through 1402 removed outlier: 3.630A pdb=" N PHE C1401 " --> pdb=" O ARG C1398 " (cutoff:3.500A) Processing helix chain 'C' and resid 1404 through 1409 removed outlier: 4.037A pdb=" N MET C1409 " --> pdb=" O PRO C1406 " (cutoff:3.500A) Processing helix chain 'C' and resid 1420 through 1424 Processing helix chain 'C' and resid 1431 through 1442 Processing helix chain 'C' and resid 1463 through 1465 No H-bonds generated for 'chain 'C' and resid 1463 through 1465' Processing helix chain 'C' and resid 1466 through 1473 Processing helix chain 'C' and resid 1494 through 1510 Processing helix chain 'C' and resid 1517 through 1520 Processing helix chain 'C' and resid 1525 through 1538 Processing helix chain 'C' and resid 1550 through 1560 Processing helix chain 'C' and resid 1568 through 1579 Processing helix chain 'C' and resid 1599 through 1608 removed outlier: 4.084A pdb=" N LEU C1603 " --> pdb=" O GLU C1599 " (cutoff:3.500A) Processing helix chain 'C' and resid 1609 through 1613 Processing helix chain 'C' and resid 1645 through 1656 Processing helix chain 'C' and resid 1703 through 1712 Processing helix chain 'C' and resid 1770 through 1792 Processing helix chain 'C' and resid 1793 through 1796 Processing helix chain 'C' and resid 1829 through 1834 Processing helix chain 'C' and resid 1835 through 1837 No H-bonds generated for 'chain 'C' and resid 1835 through 1837' Processing helix chain 'C' and resid 1853 through 1855 No H-bonds generated for 'chain 'C' and resid 1853 through 1855' Processing helix chain 'C' and resid 1881 through 1885 Processing helix chain 'C' and resid 1914 through 1926 removed outlier: 4.055A pdb=" N HIS C1926 " --> pdb=" O VAL C1922 " (cutoff:3.500A) Processing helix chain 'C' and resid 1954 through 1961 removed outlier: 3.733A pdb=" N LEU C1958 " --> pdb=" O SER C1954 " (cutoff:3.500A) Processing helix chain 'C' and resid 1962 through 1966 Processing helix chain 'C' and resid 1967 through 1988 Processing helix chain 'C' and resid 1996 through 1998 No H-bonds generated for 'chain 'C' and resid 1996 through 1998' Processing helix chain 'C' and resid 2040 through 2045 Processing helix chain 'C' and resid 2051 through 2068 removed outlier: 3.825A pdb=" N ASP C2055 " --> pdb=" O ASN C2051 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL C2056 " --> pdb=" O GLN C2052 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR C2057 " --> pdb=" O GLN C2053 " (cutoff:3.500A) Processing helix chain 'C' and resid 2094 through 2099 Processing helix chain 'C' and resid 2104 through 2114 Processing helix chain 'C' and resid 2118 through 2122 Processing helix chain 'C' and resid 2124 through 2132 Processing helix chain 'C' and resid 2134 through 2139 removed outlier: 3.689A pdb=" N VAL C2138 " --> pdb=" O SER C2134 " (cutoff:3.500A) Processing helix chain 'C' and resid 2278 through 2282 removed outlier: 3.714A pdb=" N LEU C2282 " --> pdb=" O THR C2279 " (cutoff:3.500A) Processing helix chain 'C' and resid 2308 through 2312 Processing helix chain 'C' and resid 2339 through 2344 removed outlier: 3.728A pdb=" N GLN C2342 " --> pdb=" O ARG C2339 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2351 Processing helix chain 'C' and resid 2389 through 2395 Processing helix chain 'C' and resid 2499 through 2526 Processing sheet with id=AA1, first strand: chain 'B' and resid 796 through 797 removed outlier: 6.707A pdb=" N ILE B 803 " --> pdb=" O ASP B 988 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 987 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU B1016 " --> pdb=" O ASP B1041 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU B1063 " --> pdb=" O ASN B1089 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE B1088 " --> pdb=" O ILE B1113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 1177 through 1179 removed outlier: 6.884A pdb=" N LEU B1178 " --> pdb=" O ASP B1202 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU B1201 " --> pdb=" O LEU B1226 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU B1225 " --> pdb=" O HIS B1251 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU B1250 " --> pdb=" O ASP B1274 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 1329 through 1331 Processing sheet with id=AA4, first strand: chain 'B' and resid 1376 through 1378 removed outlier: 9.037A pdb=" N ILE B1448 " --> pdb=" O ALA B1413 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N TYR B1415 " --> pdb=" O ILE B1448 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N VAL B1450 " --> pdb=" O TYR B1415 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA B1417 " --> pdb=" O VAL B1450 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL B1447 " --> pdb=" O ILE B1482 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP B1484 " --> pdb=" O VAL B1447 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1548 through 1549 Processing sheet with id=AA6, first strand: chain 'B' and resid 1730 through 1731 removed outlier: 7.231A pdb=" N TYR B1747 " --> pdb=" O PRO B1768 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE B1692 " --> pdb=" O LEU B1813 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B1813 " --> pdb=" O ILE B1692 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1840 through 1841 Processing sheet with id=AA8, first strand: chain 'B' and resid 1893 through 1898 removed outlier: 6.662A pdb=" N MET B1944 " --> pdb=" O ALA B1938 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ALA B1938 " --> pdb=" O MET B1944 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B1946 " --> pdb=" O LEU B1936 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 2000 through 2002 Processing sheet with id=AB1, first strand: chain 'B' and resid 2140 through 2146 removed outlier: 6.530A pdb=" N LEU B2140 " --> pdb=" O ASP B2497 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASP B2497 " --> pdb=" O LEU B2140 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG B2142 " --> pdb=" O VAL B2495 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N SER B2491 " --> pdb=" O LEU B2146 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N TYR B2475 " --> pdb=" O VAL B2455 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL B2455 " --> pdb=" O TYR B2475 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 2170 through 2172 Processing sheet with id=AB3, first strand: chain 'B' and resid 2199 through 2207 removed outlier: 3.810A pdb=" N CYS B2201 " --> pdb=" O GLY B2218 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B2225 " --> pdb=" O SER B2217 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B2223 " --> pdb=" O THR B2219 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B2226 " --> pdb=" O HIS B2236 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 2245 through 2251 removed outlier: 3.768A pdb=" N PHE B2262 " --> pdb=" O ASN B2251 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B2273 " --> pdb=" O VAL B2265 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LYS B2271 " --> pdb=" O THR B2267 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS B2289 " --> pdb=" O ILE B2274 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 2304 through 2305 removed outlier: 3.710A pdb=" N TRP B2316 " --> pdb=" O SER B2304 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE B2323 " --> pdb=" O LEU B2335 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU B2335 " --> pdb=" O ILE B2323 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER B2325 " --> pdb=" O GLN B2333 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 2354 through 2358 removed outlier: 6.653A pdb=" N ALA B2366 " --> pdb=" O ILE B2355 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL B2357 " --> pdb=" O TYR B2364 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TYR B2364 " --> pdb=" O VAL B2357 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LYS B2367 " --> pdb=" O VAL B2372 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B2372 " --> pdb=" O LYS B2367 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP B2377 " --> pdb=" O LEU B2383 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B2383 " --> pdb=" O ASP B2377 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 2414 through 2420 removed outlier: 3.689A pdb=" N ALA B2424 " --> pdb=" O GLN B2420 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG B2446 " --> pdb=" O LEU B2436 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ASP B2438 " --> pdb=" O LEU B2444 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU B2444 " --> pdb=" O ASP B2438 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 796 through 797 removed outlier: 6.712A pdb=" N ILE C 803 " --> pdb=" O ASP C 988 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU C 987 " --> pdb=" O GLU C1017 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU C1016 " --> pdb=" O ASP C1041 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU C1063 " --> pdb=" O ASN C1089 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE C1088 " --> pdb=" O ILE C1113 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1177 through 1179 removed outlier: 6.885A pdb=" N LEU C1178 " --> pdb=" O ASP C1202 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU C1201 " --> pdb=" O LEU C1226 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU C1225 " --> pdb=" O HIS C1251 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU C1250 " --> pdb=" O ASP C1274 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 1329 through 1331 Processing sheet with id=AC2, first strand: chain 'C' and resid 1376 through 1378 removed outlier: 9.039A pdb=" N ILE C1448 " --> pdb=" O ALA C1413 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N TYR C1415 " --> pdb=" O ILE C1448 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL C1450 " --> pdb=" O TYR C1415 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ALA C1417 " --> pdb=" O VAL C1450 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL C1447 " --> pdb=" O ILE C1482 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP C1484 " --> pdb=" O VAL C1447 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1548 through 1549 Processing sheet with id=AC4, first strand: chain 'C' and resid 1730 through 1731 removed outlier: 7.238A pdb=" N TYR C1747 " --> pdb=" O PRO C1768 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE C1692 " --> pdb=" O LEU C1813 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C1813 " --> pdb=" O ILE C1692 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 1840 through 1841 Processing sheet with id=AC6, first strand: chain 'C' and resid 1893 through 1898 removed outlier: 6.664A pdb=" N MET C1944 " --> pdb=" O ALA C1938 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ALA C1938 " --> pdb=" O MET C1944 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C1946 " --> pdb=" O LEU C1936 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 2000 through 2002 Processing sheet with id=AC8, first strand: chain 'C' and resid 2140 through 2146 removed outlier: 6.541A pdb=" N LEU C2140 " --> pdb=" O ASP C2497 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASP C2497 " --> pdb=" O LEU C2140 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG C2142 " --> pdb=" O VAL C2495 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER C2491 " --> pdb=" O LEU C2146 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TYR C2475 " --> pdb=" O VAL C2455 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N VAL C2455 " --> pdb=" O TYR C2475 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 2170 through 2172 Processing sheet with id=AD1, first strand: chain 'C' and resid 2199 through 2207 removed outlier: 3.808A pdb=" N CYS C2201 " --> pdb=" O GLY C2218 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C2225 " --> pdb=" O SER C2217 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR C2223 " --> pdb=" O THR C2219 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C2226 " --> pdb=" O HIS C2236 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 2245 through 2251 removed outlier: 3.766A pdb=" N PHE C2262 " --> pdb=" O ASN C2251 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA C2273 " --> pdb=" O VAL C2265 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS C2271 " --> pdb=" O THR C2267 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS C2289 " --> pdb=" O ILE C2274 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 2304 through 2305 removed outlier: 3.708A pdb=" N TRP C2316 " --> pdb=" O SER C2304 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE C2323 " --> pdb=" O LEU C2335 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU C2335 " --> pdb=" O ILE C2323 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER C2325 " --> pdb=" O GLN C2333 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 2354 through 2358 removed outlier: 6.652A pdb=" N ALA C2366 " --> pdb=" O ILE C2355 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL C2357 " --> pdb=" O TYR C2364 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TYR C2364 " --> pdb=" O VAL C2357 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LYS C2367 " --> pdb=" O VAL C2372 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL C2372 " --> pdb=" O LYS C2367 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP C2377 " --> pdb=" O LEU C2383 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU C2383 " --> pdb=" O ASP C2377 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 2414 through 2420 removed outlier: 3.677A pdb=" N ALA C2424 " --> pdb=" O GLN C2420 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG C2446 " --> pdb=" O LEU C2436 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ASP C2438 " --> pdb=" O LEU C2444 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU C2444 " --> pdb=" O ASP C2438 " (cutoff:3.500A) 991 hydrogen bonds defined for protein. 2685 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: 6.36 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6355 1.33 - 1.45: 4181 1.45 - 1.57: 14138 1.57 - 1.69: 6 1.69 - 1.81: 206 Bond restraints: 24886 Sorted by residual: bond pdb=" CB VAL B1767 " pdb=" CG1 VAL B1767 " ideal model delta sigma weight residual 1.521 1.416 0.105 3.30e-02 9.18e+02 1.01e+01 bond pdb=" C16 0LI B2601 " pdb=" C17 0LI B2601 " ideal model delta sigma weight residual 1.402 1.461 -0.059 2.00e-02 2.50e+03 8.58e+00 bond pdb=" C16 0LI C2601 " pdb=" C17 0LI C2601 " ideal model delta sigma weight residual 1.402 1.460 -0.058 2.00e-02 2.50e+03 8.43e+00 bond pdb=" C15 0LI C2601 " pdb=" C16 0LI C2601 " ideal model delta sigma weight residual 1.388 1.445 -0.057 2.00e-02 2.50e+03 8.15e+00 bond pdb=" C15 0LI B2601 " pdb=" C16 0LI B2601 " ideal model delta sigma weight residual 1.388 1.445 -0.057 2.00e-02 2.50e+03 8.04e+00 ... (remaining 24881 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 33185 2.25 - 4.51: 728 4.51 - 6.76: 96 6.76 - 9.02: 17 9.02 - 11.27: 10 Bond angle restraints: 34036 Sorted by residual: angle pdb=" N LYS C1184 " pdb=" CA LYS C1184 " pdb=" C LYS C1184 " ideal model delta sigma weight residual 111.39 118.84 -7.45 1.38e+00 5.25e-01 2.92e+01 angle pdb=" N LYS B1184 " pdb=" CA LYS B1184 " pdb=" C LYS B1184 " ideal model delta sigma weight residual 111.39 118.81 -7.42 1.38e+00 5.25e-01 2.89e+01 angle pdb=" N VAL C1340 " pdb=" CA VAL C1340 " pdb=" CB VAL C1340 " ideal model delta sigma weight residual 111.91 104.13 7.78 1.92e+00 2.71e-01 1.64e+01 angle pdb=" N VAL B1340 " pdb=" CA VAL B1340 " pdb=" CB VAL B1340 " ideal model delta sigma weight residual 111.91 104.14 7.77 1.92e+00 2.71e-01 1.64e+01 angle pdb=" CG1 VAL B1767 " pdb=" CB VAL B1767 " pdb=" CG2 VAL B1767 " ideal model delta sigma weight residual 110.80 102.79 8.01 2.20e+00 2.07e-01 1.32e+01 ... (remaining 34031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.03: 14375 29.03 - 58.07: 453 58.07 - 87.10: 18 87.10 - 116.13: 0 116.13 - 145.17: 2 Dihedral angle restraints: 14848 sinusoidal: 4884 harmonic: 9964 Sorted by residual: dihedral pdb=" CA ASN B1867 " pdb=" C ASN B1867 " pdb=" N ILE B1868 " pdb=" CA ILE B1868 " ideal model delta harmonic sigma weight residual -180.00 -155.53 -24.47 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ASN C1867 " pdb=" C ASN C1867 " pdb=" N ILE C1868 " pdb=" CA ILE C1868 " ideal model delta harmonic sigma weight residual 180.00 -155.56 -24.44 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA TYR C1733 " pdb=" C TYR C1733 " pdb=" N TRP C1734 " pdb=" CA TRP C1734 " ideal model delta harmonic sigma weight residual 180.00 157.65 22.35 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 14845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3508 0.068 - 0.137: 670 0.137 - 0.205: 60 0.205 - 0.273: 6 0.273 - 0.341: 4 Chirality restraints: 4248 Sorted by residual: chirality pdb=" CB ILE C1738 " pdb=" CA ILE C1738 " pdb=" CG1 ILE C1738 " pdb=" CG2 ILE C1738 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB ILE B1738 " pdb=" CA ILE B1738 " pdb=" CG1 ILE B1738 " pdb=" CG2 ILE B1738 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CG LEU B 791 " pdb=" CB LEU B 791 " pdb=" CD1 LEU B 791 " pdb=" CD2 LEU B 791 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 4245 not shown) Planarity restraints: 4248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 0LI C2601 " 0.025 2.00e-02 2.50e+03 2.57e-02 1.65e+01 pdb=" C11 0LI C2601 " 0.013 2.00e-02 2.50e+03 pdb=" C12 0LI C2601 " 0.000 2.00e-02 2.50e+03 pdb=" C3 0LI C2601 " -0.055 2.00e-02 2.50e+03 pdb=" C4 0LI C2601 " 0.033 2.00e-02 2.50e+03 pdb=" C5 0LI C2601 " 0.028 2.00e-02 2.50e+03 pdb=" C6 0LI C2601 " 0.003 2.00e-02 2.50e+03 pdb=" C7 0LI C2601 " -0.016 2.00e-02 2.50e+03 pdb=" C8 0LI C2601 " -0.023 2.00e-02 2.50e+03 pdb=" C9 0LI C2601 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 0LI B2601 " 0.014 2.00e-02 2.50e+03 2.17e-02 1.17e+01 pdb=" C11 0LI B2601 " 0.004 2.00e-02 2.50e+03 pdb=" C12 0LI B2601 " -0.006 2.00e-02 2.50e+03 pdb=" C3 0LI B2601 " -0.047 2.00e-02 2.50e+03 pdb=" C4 0LI B2601 " 0.038 2.00e-02 2.50e+03 pdb=" C5 0LI B2601 " 0.019 2.00e-02 2.50e+03 pdb=" C6 0LI B2601 " 0.005 2.00e-02 2.50e+03 pdb=" C7 0LI B2601 " -0.015 2.00e-02 2.50e+03 pdb=" C8 0LI B2601 " -0.012 2.00e-02 2.50e+03 pdb=" C9 0LI B2601 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B1183 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.10e+00 pdb=" C ASN B1183 " 0.049 2.00e-02 2.50e+03 pdb=" O ASN B1183 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS B1184 " -0.017 2.00e-02 2.50e+03 ... (remaining 4245 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1009 2.71 - 3.26: 24912 3.26 - 3.81: 37733 3.81 - 4.35: 46795 4.35 - 4.90: 79154 Nonbonded interactions: 189603 Sorted by model distance: nonbonded pdb=" OG1 THR B1368 " pdb=" O3B GDP B2602 " model vdw 2.166 3.040 nonbonded pdb=" OG1 THR C1368 " pdb=" O3B GDP C2602 " model vdw 2.167 3.040 nonbonded pdb=" O THR C1912 " pdb=" NH1 ARG C1943 " model vdw 2.195 3.120 nonbonded pdb=" O THR B1912 " pdb=" NH1 ARG B1943 " model vdw 2.195 3.120 nonbonded pdb=" O LEU C1927 " pdb=" OH TYR C1984 " model vdw 2.207 3.040 ... (remaining 189598 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: 0.06 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 24.400 Find NCS groups from input model: 0.200 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 0.105 24886 Z= 0.329 Angle : 0.827 11.270 34036 Z= 0.420 Chirality : 0.053 0.341 4248 Planarity : 0.005 0.047 4248 Dihedral : 14.054 145.169 8340 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.87 % Favored : 93.07 % Rotamer: Outliers : 0.17 % Allowed : 19.68 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.13), residues: 3346 helix: -1.19 (0.14), residues: 1054 sheet: -2.91 (0.18), residues: 672 loop : -2.33 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1915 TYR 0.019 0.002 TYR B1733 PHE 0.022 0.002 PHE C1185 TRP 0.030 0.003 TRP B1434 HIS 0.007 0.001 HIS B2510 Details of bonding type rmsd covalent geometry : bond 0.00793 (24886) covalent geometry : angle 0.82666 (34036) hydrogen bonds : bond 0.19631 ( 991) hydrogen bonds : angle 7.22544 ( 2685) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 324 time to evaluate : 0.761 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: B 694 LEU cc_start: 0.9211 (mt) cc_final: 0.8992 (pp) REVERT: B 1947 MET cc_start: 0.8188 (mtp) cc_final: 0.7539 (mmm) REVERT: B 2004 THR cc_start: 0.8621 (t) cc_final: 0.8344 (m) REVERT: B 2315 MET cc_start: 0.7271 (mpp) cc_final: 0.6358 (mpp) REVERT: B 2393 LEU cc_start: 0.7586 (mm) cc_final: 0.7377 (tt) REVERT: B 2496 TRP cc_start: 0.8606 (m100) cc_final: 0.8397 (m100) REVERT: C 694 LEU cc_start: 0.9146 (mt) cc_final: 0.8903 (pp) REVERT: C 1788 MET cc_start: 0.8828 (mmm) cc_final: 0.8479 (mmm) REVERT: C 1947 MET cc_start: 0.8239 (mtp) cc_final: 0.7620 (mmm) REVERT: C 2004 THR cc_start: 0.8668 (t) cc_final: 0.8419 (m) REVERT: C 2315 MET cc_start: 0.7299 (mpp) cc_final: 0.6522 (mpp) REVERT: C 2393 LEU cc_start: 0.7568 (mm) cc_final: 0.7359 (tt) outliers start: 4 outliers final: 0 residues processed: 328 average time/residue: 0.1579 time to fit residues: 83.0297 Evaluate side-chains 180 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN ** C2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2510 HIS ** 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 = 0.4085 r_free = 0.4085 target = 0.113366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.084129 restraints weight = 69626.189| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 3.70 r_work: 0.3354 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24886 Z= 0.149 Angle : 0.633 8.776 34036 Z= 0.318 Chirality : 0.044 0.172 4248 Planarity : 0.004 0.065 4248 Dihedral : 5.638 55.229 3594 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.10 % Favored : 93.84 % Rotamer: Outliers : 2.35 % Allowed : 19.73 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.14), residues: 3346 helix: 0.09 (0.16), residues: 1084 sheet: -2.40 (0.19), residues: 656 loop : -1.78 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B2122 TYR 0.014 0.001 TYR C 707 PHE 0.014 0.001 PHE C1883 TRP 0.021 0.002 TRP C2496 HIS 0.007 0.001 HIS C2510 Details of bonding type rmsd covalent geometry : bond 0.00333 (24886) covalent geometry : angle 0.63311 (34036) hydrogen bonds : bond 0.04073 ( 991) hydrogen bonds : angle 5.13450 ( 2685) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 202 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 649 PHE cc_start: 0.8563 (m-80) cc_final: 0.8253 (m-80) REVERT: B 694 LEU cc_start: 0.9326 (mt) cc_final: 0.8993 (pp) REVERT: B 1057 MET cc_start: 0.8515 (mpp) cc_final: 0.8234 (mpp) REVERT: B 1947 MET cc_start: 0.8145 (mtp) cc_final: 0.7685 (mmm) REVERT: B 2004 THR cc_start: 0.8868 (t) cc_final: 0.8580 (m) REVERT: B 2155 MET cc_start: 0.7172 (ptp) cc_final: 0.6910 (ptp) REVERT: B 2264 LEU cc_start: 0.9305 (mt) cc_final: 0.9097 (mt) REVERT: B 2272 LEU cc_start: 0.6660 (tp) cc_final: 0.6416 (mt) REVERT: B 2496 TRP cc_start: 0.8529 (m100) cc_final: 0.7809 (m100) REVERT: C 649 PHE cc_start: 0.8580 (m-80) cc_final: 0.8256 (m-80) REVERT: C 694 LEU cc_start: 0.9390 (mt) cc_final: 0.9106 (pp) REVERT: C 1057 MET cc_start: 0.8490 (mpp) cc_final: 0.8210 (mpp) REVERT: C 1697 MET cc_start: 0.8996 (ptp) cc_final: 0.8443 (mtm) REVERT: C 1947 MET cc_start: 0.8161 (mtp) cc_final: 0.7683 (mmm) REVERT: C 2004 THR cc_start: 0.8868 (t) cc_final: 0.8569 (m) REVERT: C 2155 MET cc_start: 0.7127 (ptp) cc_final: 0.6867 (ptp) REVERT: C 2272 LEU cc_start: 0.6646 (tp) cc_final: 0.6132 (mt) REVERT: C 2303 LEU cc_start: 0.6029 (OUTLIER) cc_final: 0.5756 (tp) REVERT: C 2315 MET cc_start: 0.6347 (mpp) cc_final: 0.6117 (mpp) REVERT: C 2419 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6726 (pp) outliers start: 55 outliers final: 22 residues processed: 248 average time/residue: 0.1406 time to fit residues: 58.5702 Evaluate side-chains 188 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain B residue 1218 LYS Chi-restraints excluded: chain B residue 1592 LEU Chi-restraints excluded: chain B residue 1853 SER Chi-restraints excluded: chain B residue 2063 LEU Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2419 LEU Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 1066 SER Chi-restraints excluded: chain C residue 1176 THR Chi-restraints excluded: chain C residue 1218 LYS Chi-restraints excluded: chain C residue 1592 LEU Chi-restraints excluded: chain C residue 1853 SER Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2303 LEU Chi-restraints excluded: chain C residue 2419 LEU Chi-restraints excluded: chain C residue 2502 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 101 optimal weight: 0.7980 chunk 67 optimal weight: 0.0470 chunk 28 optimal weight: 5.9990 chunk 309 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 275 optimal weight: 1.9990 chunk 316 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 282 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 721 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.112676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.082698 restraints weight = 69444.247| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.71 r_work: 0.3319 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24886 Z= 0.142 Angle : 0.605 9.705 34036 Z= 0.299 Chirality : 0.043 0.183 4248 Planarity : 0.004 0.050 4248 Dihedral : 5.282 53.217 3594 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.98 % Favored : 93.96 % Rotamer: Outliers : 2.13 % Allowed : 20.84 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.15), residues: 3346 helix: 0.58 (0.16), residues: 1084 sheet: -2.10 (0.19), residues: 650 loop : -1.48 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 715 TYR 0.012 0.001 TYR C1739 PHE 0.010 0.001 PHE C1877 TRP 0.012 0.001 TRP B1705 HIS 0.005 0.001 HIS B2510 Details of bonding type rmsd covalent geometry : bond 0.00326 (24886) covalent geometry : angle 0.60530 (34036) hydrogen bonds : bond 0.03599 ( 991) hydrogen bonds : angle 4.69631 ( 2685) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 564 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7617 (pp) REVERT: B 649 PHE cc_start: 0.8575 (m-80) cc_final: 0.8259 (m-80) REVERT: B 694 LEU cc_start: 0.9328 (mt) cc_final: 0.8996 (pp) REVERT: B 997 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7664 (tt) REVERT: B 1057 MET cc_start: 0.8427 (mpp) cc_final: 0.8167 (mmt) REVERT: B 1947 MET cc_start: 0.8145 (mtp) cc_final: 0.7697 (mmm) REVERT: B 2315 MET cc_start: 0.6379 (mpp) cc_final: 0.6146 (mpp) REVERT: B 2459 MET cc_start: 0.6821 (ttp) cc_final: 0.6232 (tmm) REVERT: C 564 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7456 (pp) REVERT: C 649 PHE cc_start: 0.8593 (m-80) cc_final: 0.8240 (m-80) REVERT: C 694 LEU cc_start: 0.9383 (mt) cc_final: 0.9095 (pp) REVERT: C 846 TYR cc_start: 0.8508 (m-10) cc_final: 0.8267 (m-80) REVERT: C 997 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7735 (tt) REVERT: C 1057 MET cc_start: 0.8400 (mpp) cc_final: 0.8144 (mmt) REVERT: C 1101 ASN cc_start: 0.6987 (OUTLIER) cc_final: 0.6746 (t0) REVERT: C 1371 ILE cc_start: 0.8164 (pt) cc_final: 0.7844 (mt) REVERT: C 1697 MET cc_start: 0.9007 (ptp) cc_final: 0.8553 (mtm) REVERT: C 1947 MET cc_start: 0.8153 (mtp) cc_final: 0.7685 (mmm) REVERT: C 2315 MET cc_start: 0.6613 (mpp) cc_final: 0.6395 (mpp) REVERT: C 2419 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6466 (pp) outliers start: 50 outliers final: 28 residues processed: 215 average time/residue: 0.1383 time to fit residues: 50.7675 Evaluate side-chains 192 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1218 LYS Chi-restraints excluded: chain B residue 1330 VAL Chi-restraints excluded: chain B residue 1592 LEU Chi-restraints excluded: chain B residue 1610 ILE Chi-restraints excluded: chain B residue 1853 SER Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2419 LEU Chi-restraints excluded: chain B residue 2434 ILE Chi-restraints excluded: chain B residue 2447 VAL Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 802 SER Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1066 SER Chi-restraints excluded: chain C residue 1101 ASN Chi-restraints excluded: chain C residue 1218 LYS Chi-restraints excluded: chain C residue 1330 VAL Chi-restraints excluded: chain C residue 1592 LEU Chi-restraints excluded: chain C residue 1610 ILE Chi-restraints excluded: chain C residue 1853 SER Chi-restraints excluded: chain C residue 2303 LEU Chi-restraints excluded: chain C residue 2358 VAL Chi-restraints excluded: chain C residue 2419 LEU Chi-restraints excluded: chain C residue 2434 ILE Chi-restraints excluded: chain C residue 2447 VAL Chi-restraints excluded: chain C residue 2500 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 119 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 287 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 247 optimal weight: 6.9990 chunk 145 optimal weight: 0.0870 chunk 300 optimal weight: 2.9990 chunk 195 optimal weight: 0.0020 chunk 153 optimal weight: 6.9990 chunk 293 optimal weight: 0.9990 overall best weight: 0.6172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1043 HIS ** C1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1043 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.111785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.079977 restraints weight = 68318.370| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 4.08 r_work: 0.3320 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24886 Z= 0.111 Angle : 0.568 9.514 34036 Z= 0.279 Chirality : 0.042 0.169 4248 Planarity : 0.003 0.044 4248 Dihedral : 5.011 52.574 3594 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.89 % Favored : 94.05 % Rotamer: Outliers : 2.31 % Allowed : 21.05 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.15), residues: 3346 helix: 0.86 (0.17), residues: 1080 sheet: -1.84 (0.20), residues: 628 loop : -1.24 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 715 TYR 0.010 0.001 TYR C1739 PHE 0.009 0.001 PHE B1883 TRP 0.012 0.001 TRP B1734 HIS 0.005 0.001 HIS B2510 Details of bonding type rmsd covalent geometry : bond 0.00253 (24886) covalent geometry : angle 0.56789 (34036) hydrogen bonds : bond 0.03173 ( 991) hydrogen bonds : angle 4.43435 ( 2685) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 166 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 649 PHE cc_start: 0.8564 (m-80) cc_final: 0.8217 (m-80) REVERT: B 694 LEU cc_start: 0.9372 (mt) cc_final: 0.9073 (pp) REVERT: B 997 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.7865 (tt) REVERT: B 1057 MET cc_start: 0.8278 (mpp) cc_final: 0.8012 (mmt) REVERT: B 1947 MET cc_start: 0.8176 (mtp) cc_final: 0.7714 (mmm) REVERT: B 2224 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8076 (tt) REVERT: B 2315 MET cc_start: 0.6348 (mpp) cc_final: 0.6064 (mpp) REVERT: B 2419 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6640 (pp) REVERT: B 2426 TRP cc_start: 0.7877 (m100) cc_final: 0.7649 (m100) REVERT: B 2459 MET cc_start: 0.6658 (ttp) cc_final: 0.6272 (tmm) REVERT: C 649 PHE cc_start: 0.8466 (m-80) cc_final: 0.8214 (m-80) REVERT: C 694 LEU cc_start: 0.9405 (mt) cc_final: 0.9109 (pp) REVERT: C 846 TYR cc_start: 0.8536 (m-10) cc_final: 0.8275 (m-80) REVERT: C 997 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.7952 (tt) REVERT: C 1057 MET cc_start: 0.8273 (mpp) cc_final: 0.7992 (mmt) REVERT: C 1101 ASN cc_start: 0.7117 (OUTLIER) cc_final: 0.6874 (t0) REVERT: C 1697 MET cc_start: 0.8972 (ptp) cc_final: 0.8589 (mtm) REVERT: C 1947 MET cc_start: 0.8166 (mtp) cc_final: 0.7678 (mmm) REVERT: C 2139 CYS cc_start: 0.8834 (m) cc_final: 0.8484 (p) REVERT: C 2224 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8016 (tt) outliers start: 54 outliers final: 30 residues processed: 206 average time/residue: 0.1478 time to fit residues: 50.9600 Evaluate side-chains 194 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1203 MET Chi-restraints excluded: chain B residue 1330 VAL Chi-restraints excluded: chain B residue 1592 LEU Chi-restraints excluded: chain B residue 1610 ILE Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1853 SER Chi-restraints excluded: chain B residue 2063 LEU Chi-restraints excluded: chain B residue 2204 LEU Chi-restraints excluded: chain B residue 2224 LEU Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2358 VAL Chi-restraints excluded: chain B residue 2419 LEU Chi-restraints excluded: chain C residue 802 SER Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1066 SER Chi-restraints excluded: chain C residue 1101 ASN Chi-restraints excluded: chain C residue 1203 MET Chi-restraints excluded: chain C residue 1330 VAL Chi-restraints excluded: chain C residue 1592 LEU Chi-restraints excluded: chain C residue 1610 ILE Chi-restraints excluded: chain C residue 1652 LEU Chi-restraints excluded: chain C residue 1853 SER Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2111 ILE Chi-restraints excluded: chain C residue 2224 LEU Chi-restraints excluded: chain C residue 2303 LEU Chi-restraints excluded: chain C residue 2419 LEU Chi-restraints excluded: chain C residue 2434 ILE Chi-restraints excluded: chain C residue 2447 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 118 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 324 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.110395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.078759 restraints weight = 68551.563| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.91 r_work: 0.3292 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24886 Z= 0.157 Angle : 0.583 8.032 34036 Z= 0.289 Chirality : 0.043 0.161 4248 Planarity : 0.003 0.042 4248 Dihedral : 5.022 53.267 3594 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.90 % Allowed : 21.52 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.15), residues: 3346 helix: 1.01 (0.17), residues: 1078 sheet: -1.65 (0.21), residues: 592 loop : -1.25 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1501 TYR 0.015 0.001 TYR C 707 PHE 0.012 0.001 PHE B1877 TRP 0.012 0.001 TRP C1705 HIS 0.006 0.001 HIS B2510 Details of bonding type rmsd covalent geometry : bond 0.00365 (24886) covalent geometry : angle 0.58311 (34036) hydrogen bonds : bond 0.03289 ( 991) hydrogen bonds : angle 4.41092 ( 2685) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 161 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 564 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7565 (pp) REVERT: B 649 PHE cc_start: 0.8492 (m-80) cc_final: 0.8261 (m-80) REVERT: B 694 LEU cc_start: 0.9355 (mt) cc_final: 0.9095 (pp) REVERT: B 997 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8029 (tt) REVERT: B 1057 MET cc_start: 0.8244 (mpp) cc_final: 0.7942 (mmt) REVERT: B 1677 ARG cc_start: 0.7374 (ppt170) cc_final: 0.6981 (ppt170) REVERT: B 1947 MET cc_start: 0.8238 (mtp) cc_final: 0.7771 (mmm) REVERT: B 2224 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8192 (tt) REVERT: B 2459 MET cc_start: 0.7100 (ttp) cc_final: 0.6358 (tmm) REVERT: C 564 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7411 (pp) REVERT: C 649 PHE cc_start: 0.8456 (m-80) cc_final: 0.8228 (m-80) REVERT: C 694 LEU cc_start: 0.9413 (mt) cc_final: 0.9158 (pp) REVERT: C 997 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8088 (tt) REVERT: C 1057 MET cc_start: 0.8239 (mpp) cc_final: 0.7931 (mmt) REVERT: C 1101 ASN cc_start: 0.7466 (OUTLIER) cc_final: 0.7145 (t0) REVERT: C 1677 ARG cc_start: 0.7362 (ppt170) cc_final: 0.6953 (ppt170) REVERT: C 1697 MET cc_start: 0.8938 (ptp) cc_final: 0.8661 (mtm) REVERT: C 1947 MET cc_start: 0.8229 (mtp) cc_final: 0.7746 (mmm) REVERT: C 2139 CYS cc_start: 0.8773 (m) cc_final: 0.8484 (p) REVERT: C 2459 MET cc_start: 0.7102 (ttp) cc_final: 0.6436 (tmm) outliers start: 68 outliers final: 43 residues processed: 214 average time/residue: 0.1418 time to fit residues: 51.0774 Evaluate side-chains 198 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 149 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1203 MET Chi-restraints excluded: chain B residue 1218 LYS Chi-restraints excluded: chain B residue 1330 VAL Chi-restraints excluded: chain B residue 1590 LEU Chi-restraints excluded: chain B residue 1592 LEU Chi-restraints excluded: chain B residue 1610 ILE Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1853 SER Chi-restraints excluded: chain B residue 2063 LEU Chi-restraints excluded: chain B residue 2111 ILE Chi-restraints excluded: chain B residue 2224 LEU Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2373 VAL Chi-restraints excluded: chain B residue 2419 LEU Chi-restraints excluded: chain B residue 2427 ILE Chi-restraints excluded: chain B residue 2434 ILE Chi-restraints excluded: chain B residue 2447 VAL Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 802 SER Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1066 SER Chi-restraints excluded: chain C residue 1101 ASN Chi-restraints excluded: chain C residue 1203 MET Chi-restraints excluded: chain C residue 1218 LYS Chi-restraints excluded: chain C residue 1330 VAL Chi-restraints excluded: chain C residue 1592 LEU Chi-restraints excluded: chain C residue 1610 ILE Chi-restraints excluded: chain C residue 1652 LEU Chi-restraints excluded: chain C residue 1853 SER Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2096 VAL Chi-restraints excluded: chain C residue 2111 ILE Chi-restraints excluded: chain C residue 2204 LEU Chi-restraints excluded: chain C residue 2303 LEU Chi-restraints excluded: chain C residue 2373 VAL Chi-restraints excluded: chain C residue 2419 LEU Chi-restraints excluded: chain C residue 2427 ILE Chi-restraints excluded: chain C residue 2434 ILE Chi-restraints excluded: chain C residue 2447 VAL Chi-restraints excluded: chain C residue 2500 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 37 optimal weight: 3.9990 chunk 306 optimal weight: 9.9990 chunk 324 optimal weight: 3.9990 chunk 187 optimal weight: 40.0000 chunk 291 optimal weight: 0.6980 chunk 229 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 309 optimal weight: 8.9990 chunk 290 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2251 ASN ** C1039 HIS ** 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 = 0.4013 r_free = 0.4013 target = 0.107974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.073581 restraints weight = 69014.370| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.10 r_work: 0.3275 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 24886 Z= 0.265 Angle : 0.675 10.967 34036 Z= 0.333 Chirality : 0.046 0.158 4248 Planarity : 0.004 0.042 4248 Dihedral : 5.302 54.514 3594 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.50 % Allowed : 22.33 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.15), residues: 3346 helix: 0.87 (0.17), residues: 1080 sheet: -1.87 (0.20), residues: 628 loop : -1.27 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C1973 TYR 0.019 0.002 TYR C1739 PHE 0.020 0.002 PHE B1877 TRP 0.016 0.002 TRP C1705 HIS 0.009 0.001 HIS C2510 Details of bonding type rmsd covalent geometry : bond 0.00620 (24886) covalent geometry : angle 0.67520 (34036) hydrogen bonds : bond 0.03703 ( 991) hydrogen bonds : angle 4.62943 ( 2685) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 148 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 564 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7573 (pp) REVERT: B 694 LEU cc_start: 0.9397 (mt) cc_final: 0.9130 (pp) REVERT: B 997 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8197 (tt) REVERT: B 1057 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7263 (mpp) REVERT: B 1237 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8201 (mp) REVERT: B 1607 MET cc_start: 0.8633 (mmp) cc_final: 0.8238 (mmp) REVERT: B 1947 MET cc_start: 0.8347 (mtp) cc_final: 0.8002 (mmm) REVERT: B 2224 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8124 (tt) REVERT: B 2419 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6738 (pp) REVERT: B 2459 MET cc_start: 0.6984 (ttp) cc_final: 0.6259 (tmm) REVERT: C 564 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7405 (pp) REVERT: C 694 LEU cc_start: 0.9409 (mt) cc_final: 0.9146 (pp) REVERT: C 997 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8244 (tt) REVERT: C 1057 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7217 (mpp) REVERT: C 1237 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8201 (mp) REVERT: C 1607 MET cc_start: 0.8590 (mmp) cc_final: 0.8353 (mmp) REVERT: C 1697 MET cc_start: 0.8868 (ptp) cc_final: 0.8622 (mtm) REVERT: C 1947 MET cc_start: 0.8340 (mtp) cc_final: 0.7990 (mmm) REVERT: C 2459 MET cc_start: 0.7022 (ttp) cc_final: 0.6249 (tmm) outliers start: 82 outliers final: 57 residues processed: 209 average time/residue: 0.1499 time to fit residues: 51.7644 Evaluate side-chains 212 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 145 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1057 MET Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1203 MET Chi-restraints excluded: chain B residue 1218 LYS Chi-restraints excluded: chain B residue 1237 LEU Chi-restraints excluded: chain B residue 1330 VAL Chi-restraints excluded: chain B residue 1590 LEU Chi-restraints excluded: chain B residue 1592 LEU Chi-restraints excluded: chain B residue 1610 ILE Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1754 VAL Chi-restraints excluded: chain B residue 1853 SER Chi-restraints excluded: chain B residue 1925 CYS Chi-restraints excluded: chain B residue 2062 LEU Chi-restraints excluded: chain B residue 2063 LEU Chi-restraints excluded: chain B residue 2096 VAL Chi-restraints excluded: chain B residue 2111 ILE Chi-restraints excluded: chain B residue 2186 THR Chi-restraints excluded: chain B residue 2204 LEU Chi-restraints excluded: chain B residue 2224 LEU Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2357 VAL Chi-restraints excluded: chain B residue 2373 VAL Chi-restraints excluded: chain B residue 2419 LEU Chi-restraints excluded: chain B residue 2427 ILE Chi-restraints excluded: chain B residue 2434 ILE Chi-restraints excluded: chain B residue 2447 VAL Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 802 SER Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1057 MET Chi-restraints excluded: chain C residue 1066 SER Chi-restraints excluded: chain C residue 1203 MET Chi-restraints excluded: chain C residue 1218 LYS Chi-restraints excluded: chain C residue 1237 LEU Chi-restraints excluded: chain C residue 1330 VAL Chi-restraints excluded: chain C residue 1355 MET Chi-restraints excluded: chain C residue 1528 VAL Chi-restraints excluded: chain C residue 1592 LEU Chi-restraints excluded: chain C residue 1610 ILE Chi-restraints excluded: chain C residue 1652 LEU Chi-restraints excluded: chain C residue 1754 VAL Chi-restraints excluded: chain C residue 1853 SER Chi-restraints excluded: chain C residue 1916 LEU Chi-restraints excluded: chain C residue 1925 CYS Chi-restraints excluded: chain C residue 2062 LEU Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2096 VAL Chi-restraints excluded: chain C residue 2111 ILE Chi-restraints excluded: chain C residue 2186 THR Chi-restraints excluded: chain C residue 2202 LEU Chi-restraints excluded: chain C residue 2204 LEU Chi-restraints excluded: chain C residue 2303 LEU Chi-restraints excluded: chain C residue 2373 VAL Chi-restraints excluded: chain C residue 2419 LEU Chi-restraints excluded: chain C residue 2427 ILE Chi-restraints excluded: chain C residue 2434 ILE Chi-restraints excluded: chain C residue 2447 VAL Chi-restraints excluded: chain C residue 2500 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 328 optimal weight: 0.5980 chunk 142 optimal weight: 0.0770 chunk 115 optimal weight: 2.9990 chunk 223 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 279 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 225 optimal weight: 0.0970 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1039 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 = 0.4047 r_free = 0.4047 target = 0.110155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.080113 restraints weight = 68532.540| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 4.08 r_work: 0.3302 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24886 Z= 0.105 Angle : 0.571 9.216 34036 Z= 0.280 Chirality : 0.042 0.149 4248 Planarity : 0.003 0.038 4248 Dihedral : 4.958 52.164 3594 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.39 % Allowed : 23.65 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.15), residues: 3346 helix: 1.06 (0.17), residues: 1078 sheet: -1.72 (0.20), residues: 632 loop : -1.04 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C1386 TYR 0.011 0.001 TYR C1419 PHE 0.014 0.001 PHE C 649 TRP 0.026 0.002 TRP B2376 HIS 0.005 0.001 HIS B1043 Details of bonding type rmsd covalent geometry : bond 0.00236 (24886) covalent geometry : angle 0.57102 (34036) hydrogen bonds : bond 0.03097 ( 991) hydrogen bonds : angle 4.36411 ( 2685) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 150 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 694 LEU cc_start: 0.9408 (mt) cc_final: 0.9133 (pp) REVERT: B 1057 MET cc_start: 0.8139 (mpp) cc_final: 0.7804 (mmt) REVERT: B 1658 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8154 (mt) REVERT: B 1947 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7510 (mmm) REVERT: B 2224 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8183 (tt) REVERT: B 2459 MET cc_start: 0.7149 (ttp) cc_final: 0.6423 (tmm) REVERT: C 679 MET cc_start: 0.8159 (mmm) cc_final: 0.7911 (mmp) REVERT: C 694 LEU cc_start: 0.9422 (mt) cc_final: 0.9151 (pp) REVERT: C 1057 MET cc_start: 0.8159 (mpp) cc_final: 0.7805 (mmt) REVERT: C 1101 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7618 (t0) REVERT: C 1697 MET cc_start: 0.8766 (ptp) cc_final: 0.8524 (mtm) REVERT: C 1947 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7504 (mmm) REVERT: C 2139 CYS cc_start: 0.8781 (m) cc_final: 0.8482 (p) REVERT: C 2459 MET cc_start: 0.7077 (ttp) cc_final: 0.6299 (tmm) outliers start: 56 outliers final: 40 residues processed: 192 average time/residue: 0.1399 time to fit residues: 45.8689 Evaluate side-chains 187 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 142 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 1203 MET Chi-restraints excluded: chain B residue 1218 LYS Chi-restraints excluded: chain B residue 1330 VAL Chi-restraints excluded: chain B residue 1592 LEU Chi-restraints excluded: chain B residue 1610 ILE Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1658 ILE Chi-restraints excluded: chain B residue 1853 SER Chi-restraints excluded: chain B residue 1925 CYS Chi-restraints excluded: chain B residue 1947 MET Chi-restraints excluded: chain B residue 2063 LEU Chi-restraints excluded: chain B residue 2111 ILE Chi-restraints excluded: chain B residue 2186 THR Chi-restraints excluded: chain B residue 2204 LEU Chi-restraints excluded: chain B residue 2224 LEU Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2419 LEU Chi-restraints excluded: chain B residue 2434 ILE Chi-restraints excluded: chain B residue 2447 VAL Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 802 SER Chi-restraints excluded: chain C residue 1101 ASN Chi-restraints excluded: chain C residue 1203 MET Chi-restraints excluded: chain C residue 1218 LYS Chi-restraints excluded: chain C residue 1330 VAL Chi-restraints excluded: chain C residue 1592 LEU Chi-restraints excluded: chain C residue 1610 ILE Chi-restraints excluded: chain C residue 1652 LEU Chi-restraints excluded: chain C residue 1754 VAL Chi-restraints excluded: chain C residue 1853 SER Chi-restraints excluded: chain C residue 1925 CYS Chi-restraints excluded: chain C residue 1947 MET Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2111 ILE Chi-restraints excluded: chain C residue 2155 MET Chi-restraints excluded: chain C residue 2186 THR Chi-restraints excluded: chain C residue 2204 LEU Chi-restraints excluded: chain C residue 2303 LEU Chi-restraints excluded: chain C residue 2419 LEU Chi-restraints excluded: chain C residue 2434 ILE Chi-restraints excluded: chain C residue 2447 VAL Chi-restraints excluded: chain C residue 2500 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 65 optimal weight: 0.0670 chunk 124 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 chunk 236 optimal weight: 0.9980 chunk 4 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 chunk 248 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1039 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 = 0.4047 r_free = 0.4047 target = 0.110185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.076490 restraints weight = 68570.776| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.12 r_work: 0.3339 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24886 Z= 0.109 Angle : 0.569 12.619 34036 Z= 0.277 Chirality : 0.042 0.147 4248 Planarity : 0.003 0.042 4248 Dihedral : 4.798 52.319 3594 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.56 % Allowed : 23.61 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.15), residues: 3346 helix: 1.11 (0.17), residues: 1080 sheet: -1.66 (0.20), residues: 636 loop : -0.95 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C1386 TYR 0.010 0.001 TYR C1739 PHE 0.010 0.001 PHE B1704 TRP 0.021 0.001 TRP C2376 HIS 0.005 0.001 HIS C2510 Details of bonding type rmsd covalent geometry : bond 0.00248 (24886) covalent geometry : angle 0.56898 (34036) hydrogen bonds : bond 0.03024 ( 991) hydrogen bonds : angle 4.30309 ( 2685) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 145 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 694 LEU cc_start: 0.9415 (mt) cc_final: 0.9138 (pp) REVERT: B 715 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8543 (mtp180) REVERT: B 1658 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8149 (mt) REVERT: B 1947 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7506 (mmm) REVERT: B 2224 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8186 (tt) REVERT: B 2419 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6731 (pp) REVERT: B 2459 MET cc_start: 0.7041 (ttp) cc_final: 0.6366 (tmm) REVERT: C 679 MET cc_start: 0.8185 (mmm) cc_final: 0.7952 (mmp) REVERT: C 694 LEU cc_start: 0.9418 (mt) cc_final: 0.9152 (pp) REVERT: C 1101 ASN cc_start: 0.8147 (OUTLIER) cc_final: 0.7797 (t0) REVERT: C 1658 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8162 (mt) REVERT: C 1947 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7499 (mmm) REVERT: C 2139 CYS cc_start: 0.8738 (m) cc_final: 0.8397 (p) REVERT: C 2365 ILE cc_start: 0.8759 (mm) cc_final: 0.8191 (pt) REVERT: C 2459 MET cc_start: 0.6833 (ttp) cc_final: 0.6033 (tmm) outliers start: 60 outliers final: 44 residues processed: 190 average time/residue: 0.1497 time to fit residues: 47.5579 Evaluate side-chains 193 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 141 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 715 ARG Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1203 MET Chi-restraints excluded: chain B residue 1218 LYS Chi-restraints excluded: chain B residue 1330 VAL Chi-restraints excluded: chain B residue 1590 LEU Chi-restraints excluded: chain B residue 1592 LEU Chi-restraints excluded: chain B residue 1610 ILE Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1658 ILE Chi-restraints excluded: chain B residue 1853 SER Chi-restraints excluded: chain B residue 1925 CYS Chi-restraints excluded: chain B residue 1947 MET Chi-restraints excluded: chain B residue 2062 LEU Chi-restraints excluded: chain B residue 2063 LEU Chi-restraints excluded: chain B residue 2111 ILE Chi-restraints excluded: chain B residue 2151 ILE Chi-restraints excluded: chain B residue 2186 THR Chi-restraints excluded: chain B residue 2204 LEU Chi-restraints excluded: chain B residue 2224 LEU Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2419 LEU Chi-restraints excluded: chain B residue 2434 ILE Chi-restraints excluded: chain B residue 2447 VAL Chi-restraints excluded: chain C residue 668 HIS Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 802 SER Chi-restraints excluded: chain C residue 1066 SER Chi-restraints excluded: chain C residue 1101 ASN Chi-restraints excluded: chain C residue 1203 MET Chi-restraints excluded: chain C residue 1218 LYS Chi-restraints excluded: chain C residue 1330 VAL Chi-restraints excluded: chain C residue 1592 LEU Chi-restraints excluded: chain C residue 1610 ILE Chi-restraints excluded: chain C residue 1652 LEU Chi-restraints excluded: chain C residue 1658 ILE Chi-restraints excluded: chain C residue 1853 SER Chi-restraints excluded: chain C residue 1925 CYS Chi-restraints excluded: chain C residue 1947 MET Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2111 ILE Chi-restraints excluded: chain C residue 2186 THR Chi-restraints excluded: chain C residue 2202 LEU Chi-restraints excluded: chain C residue 2204 LEU Chi-restraints excluded: chain C residue 2303 LEU Chi-restraints excluded: chain C residue 2419 LEU Chi-restraints excluded: chain C residue 2434 ILE Chi-restraints excluded: chain C residue 2447 VAL Chi-restraints excluded: chain C residue 2500 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 284 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 148 optimal weight: 8.9990 chunk 238 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 194 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1039 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 = 0.4045 r_free = 0.4045 target = 0.110082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.076398 restraints weight = 68750.916| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.12 r_work: 0.3337 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24886 Z= 0.122 Angle : 0.574 9.705 34036 Z= 0.282 Chirality : 0.042 0.214 4248 Planarity : 0.003 0.037 4248 Dihedral : 4.795 52.561 3594 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.95 % Allowed : 22.93 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 3346 helix: 1.12 (0.17), residues: 1080 sheet: -1.59 (0.21), residues: 632 loop : -0.94 (0.16), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1386 TYR 0.011 0.001 TYR B1419 PHE 0.015 0.001 PHE C2326 TRP 0.021 0.001 TRP C2426 HIS 0.005 0.001 HIS B2510 Details of bonding type rmsd covalent geometry : bond 0.00281 (24886) covalent geometry : angle 0.57369 (34036) hydrogen bonds : bond 0.03024 ( 991) hydrogen bonds : angle 4.30967 ( 2685) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 140 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 694 LEU cc_start: 0.9422 (mt) cc_final: 0.9136 (pp) REVERT: B 715 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8562 (mtp180) REVERT: B 1057 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.6923 (mpp) REVERT: B 1658 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8157 (mt) REVERT: B 1947 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7510 (mmm) REVERT: B 2224 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8191 (tt) REVERT: B 2419 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6731 (pp) REVERT: B 2459 MET cc_start: 0.6838 (ttp) cc_final: 0.6270 (tmm) REVERT: C 679 MET cc_start: 0.8192 (mmm) cc_final: 0.7963 (mmp) REVERT: C 694 LEU cc_start: 0.9421 (mt) cc_final: 0.9155 (pp) REVERT: C 1057 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.6909 (mpp) REVERT: C 1101 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7818 (t0) REVERT: C 1658 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8167 (mt) REVERT: C 1947 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7500 (mmm) REVERT: C 2139 CYS cc_start: 0.8738 (m) cc_final: 0.8394 (p) REVERT: C 2365 ILE cc_start: 0.8754 (mm) cc_final: 0.8183 (pt) REVERT: C 2459 MET cc_start: 0.6637 (ttp) cc_final: 0.5969 (tmm) outliers start: 69 outliers final: 54 residues processed: 190 average time/residue: 0.1477 time to fit residues: 47.6232 Evaluate side-chains 203 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 139 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 715 ARG Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 1057 MET Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1203 MET Chi-restraints excluded: chain B residue 1218 LYS Chi-restraints excluded: chain B residue 1330 VAL Chi-restraints excluded: chain B residue 1528 VAL Chi-restraints excluded: chain B residue 1573 VAL Chi-restraints excluded: chain B residue 1590 LEU Chi-restraints excluded: chain B residue 1592 LEU Chi-restraints excluded: chain B residue 1610 ILE Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1658 ILE Chi-restraints excluded: chain B residue 1853 SER Chi-restraints excluded: chain B residue 1925 CYS Chi-restraints excluded: chain B residue 1947 MET Chi-restraints excluded: chain B residue 2063 LEU Chi-restraints excluded: chain B residue 2111 ILE Chi-restraints excluded: chain B residue 2151 ILE Chi-restraints excluded: chain B residue 2155 MET Chi-restraints excluded: chain B residue 2186 THR Chi-restraints excluded: chain B residue 2204 LEU Chi-restraints excluded: chain B residue 2224 LEU Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2419 LEU Chi-restraints excluded: chain B residue 2434 ILE Chi-restraints excluded: chain B residue 2447 VAL Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 802 SER Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 1007 SER Chi-restraints excluded: chain C residue 1057 MET Chi-restraints excluded: chain C residue 1066 SER Chi-restraints excluded: chain C residue 1101 ASN Chi-restraints excluded: chain C residue 1203 MET Chi-restraints excluded: chain C residue 1218 LYS Chi-restraints excluded: chain C residue 1330 VAL Chi-restraints excluded: chain C residue 1528 VAL Chi-restraints excluded: chain C residue 1573 VAL Chi-restraints excluded: chain C residue 1592 LEU Chi-restraints excluded: chain C residue 1610 ILE Chi-restraints excluded: chain C residue 1652 LEU Chi-restraints excluded: chain C residue 1658 ILE Chi-restraints excluded: chain C residue 1853 SER Chi-restraints excluded: chain C residue 1925 CYS Chi-restraints excluded: chain C residue 1947 MET Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2111 ILE Chi-restraints excluded: chain C residue 2151 ILE Chi-restraints excluded: chain C residue 2155 MET Chi-restraints excluded: chain C residue 2186 THR Chi-restraints excluded: chain C residue 2202 LEU Chi-restraints excluded: chain C residue 2204 LEU Chi-restraints excluded: chain C residue 2248 LEU Chi-restraints excluded: chain C residue 2303 LEU Chi-restraints excluded: chain C residue 2419 LEU Chi-restraints excluded: chain C residue 2434 ILE Chi-restraints excluded: chain C residue 2447 VAL Chi-restraints excluded: chain C residue 2470 MET Chi-restraints excluded: chain C residue 2500 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 81 optimal weight: 0.7980 chunk 330 optimal weight: 10.0000 chunk 158 optimal weight: 0.0020 chunk 118 optimal weight: 0.6980 chunk 44 optimal weight: 0.0870 chunk 124 optimal weight: 0.5980 chunk 173 optimal weight: 0.9980 chunk 282 optimal weight: 0.0370 chunk 229 optimal weight: 0.9990 chunk 196 optimal weight: 6.9990 chunk 268 optimal weight: 2.9990 overall best weight: 0.2844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1039 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 = 0.4045 r_free = 0.4045 target = 0.110065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.076394 restraints weight = 68444.968| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.10 r_work: 0.3337 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24886 Z= 0.122 Angle : 0.574 9.705 34036 Z= 0.282 Chirality : 0.042 0.214 4248 Planarity : 0.003 0.037 4248 Dihedral : 4.795 52.561 3594 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.73 % Allowed : 23.27 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 3346 helix: 1.12 (0.17), residues: 1080 sheet: -1.59 (0.21), residues: 632 loop : -0.94 (0.16), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1386 TYR 0.011 0.001 TYR B1419 PHE 0.015 0.001 PHE C2326 TRP 0.021 0.001 TRP C2426 HIS 0.005 0.001 HIS B2510 Details of bonding type rmsd covalent geometry : bond 0.00281 (24886) covalent geometry : angle 0.57368 (34036) hydrogen bonds : bond 0.03024 ( 991) hydrogen bonds : angle 4.30968 ( 2685) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 139 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 694 LEU cc_start: 0.9419 (mt) cc_final: 0.9136 (pp) REVERT: B 715 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8554 (mtp180) REVERT: B 1057 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.6926 (mpp) REVERT: B 1658 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8159 (mt) REVERT: B 1947 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7517 (mmm) REVERT: B 2224 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8187 (tt) REVERT: B 2419 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6738 (pp) REVERT: B 2459 MET cc_start: 0.6819 (ttp) cc_final: 0.6250 (tmm) REVERT: C 679 MET cc_start: 0.8200 (mmm) cc_final: 0.7963 (mmp) REVERT: C 694 LEU cc_start: 0.9419 (mt) cc_final: 0.9155 (pp) REVERT: C 1057 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.6913 (mpp) REVERT: C 1101 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7818 (t0) REVERT: C 1658 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8169 (mt) REVERT: C 1947 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7503 (mmm) REVERT: C 2139 CYS cc_start: 0.8746 (m) cc_final: 0.8397 (p) REVERT: C 2365 ILE cc_start: 0.8741 (mm) cc_final: 0.8170 (pt) REVERT: C 2459 MET cc_start: 0.6617 (ttp) cc_final: 0.5949 (tmm) outliers start: 64 outliers final: 54 residues processed: 186 average time/residue: 0.1488 time to fit residues: 46.2236 Evaluate side-chains 203 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 139 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 715 ARG Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 1057 MET Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1203 MET Chi-restraints excluded: chain B residue 1218 LYS Chi-restraints excluded: chain B residue 1330 VAL Chi-restraints excluded: chain B residue 1528 VAL Chi-restraints excluded: chain B residue 1573 VAL Chi-restraints excluded: chain B residue 1590 LEU Chi-restraints excluded: chain B residue 1592 LEU Chi-restraints excluded: chain B residue 1610 ILE Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1658 ILE Chi-restraints excluded: chain B residue 1853 SER Chi-restraints excluded: chain B residue 1925 CYS Chi-restraints excluded: chain B residue 1947 MET Chi-restraints excluded: chain B residue 2063 LEU Chi-restraints excluded: chain B residue 2111 ILE Chi-restraints excluded: chain B residue 2151 ILE Chi-restraints excluded: chain B residue 2155 MET Chi-restraints excluded: chain B residue 2186 THR Chi-restraints excluded: chain B residue 2204 LEU Chi-restraints excluded: chain B residue 2224 LEU Chi-restraints excluded: chain B residue 2303 LEU Chi-restraints excluded: chain B residue 2419 LEU Chi-restraints excluded: chain B residue 2434 ILE Chi-restraints excluded: chain B residue 2447 VAL Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 802 SER Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 1007 SER Chi-restraints excluded: chain C residue 1057 MET Chi-restraints excluded: chain C residue 1066 SER Chi-restraints excluded: chain C residue 1101 ASN Chi-restraints excluded: chain C residue 1203 MET Chi-restraints excluded: chain C residue 1218 LYS Chi-restraints excluded: chain C residue 1330 VAL Chi-restraints excluded: chain C residue 1528 VAL Chi-restraints excluded: chain C residue 1573 VAL Chi-restraints excluded: chain C residue 1592 LEU Chi-restraints excluded: chain C residue 1610 ILE Chi-restraints excluded: chain C residue 1652 LEU Chi-restraints excluded: chain C residue 1658 ILE Chi-restraints excluded: chain C residue 1853 SER Chi-restraints excluded: chain C residue 1925 CYS Chi-restraints excluded: chain C residue 1947 MET Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2111 ILE Chi-restraints excluded: chain C residue 2151 ILE Chi-restraints excluded: chain C residue 2155 MET Chi-restraints excluded: chain C residue 2186 THR Chi-restraints excluded: chain C residue 2202 LEU Chi-restraints excluded: chain C residue 2204 LEU Chi-restraints excluded: chain C residue 2248 LEU Chi-restraints excluded: chain C residue 2303 LEU Chi-restraints excluded: chain C residue 2419 LEU Chi-restraints excluded: chain C residue 2434 ILE Chi-restraints excluded: chain C residue 2447 VAL Chi-restraints excluded: chain C residue 2470 MET Chi-restraints excluded: chain C residue 2500 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 300 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 256 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 113 optimal weight: 0.3980 chunk 71 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 298 optimal weight: 0.2980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1039 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 = 0.4045 r_free = 0.4045 target = 0.110064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.076371 restraints weight = 68806.827| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.12 r_work: 0.3336 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24886 Z= 0.121 Angle : 0.574 9.693 34036 Z= 0.282 Chirality : 0.042 0.213 4248 Planarity : 0.003 0.037 4248 Dihedral : 4.798 52.561 3594 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.73 % Allowed : 23.27 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 3346 helix: 1.12 (0.17), residues: 1080 sheet: -1.59 (0.21), residues: 632 loop : -0.94 (0.16), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1386 TYR 0.011 0.001 TYR B1419 PHE 0.014 0.001 PHE C2326 TRP 0.020 0.001 TRP C2426 HIS 0.005 0.001 HIS B2510 Details of bonding type rmsd covalent geometry : bond 0.00281 (24886) covalent geometry : angle 0.57351 (34036) hydrogen bonds : bond 0.03024 ( 991) hydrogen bonds : angle 4.30981 ( 2685) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5936.75 seconds wall clock time: 102 minutes 18.24 seconds (6138.24 seconds total)