Starting phenix.real_space_refine on Thu Jan 15 09:26:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7l_41985/01_2026/8u7l_41985.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7l_41985/01_2026/8u7l_41985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u7l_41985/01_2026/8u7l_41985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7l_41985/01_2026/8u7l_41985.map" model { file = "/net/cci-nas-00/data/ceres_data/8u7l_41985/01_2026/8u7l_41985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7l_41985/01_2026/8u7l_41985.cif" } resolution = 3.6 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= 0.002 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 140 5.16 5 C 15608 2.51 5 N 4154 2.21 5 O 4310 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 24222 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 12044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1705, 12044 Classifications: {'peptide': 1705} Incomplete info: {'truncation_to_alanine': 402} Link IDs: {'PCIS': 2, 'PTRANS': 71, 'TRANS': 1631} Chain breaks: 15 Unresolved non-hydrogen bonds: 1527 Unresolved non-hydrogen angles: 1866 Unresolved non-hydrogen dihedrals: 1252 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 33, 'HIS:plan': 13, 'PHE:plan': 8, 'ASP:plan': 48, 'TYR:plan': 5, 'GLU:plan': 75, 'ARG:plan': 33, 'ASN:plan1': 24, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 970 Chain: "A" Number of atoms: 12044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1705, 12044 Classifications: {'peptide': 1705} Incomplete info: {'truncation_to_alanine': 402} Link IDs: {'PCIS': 2, 'PTRANS': 71, 'TRANS': 1631} Chain breaks: 15 Unresolved non-hydrogen bonds: 1527 Unresolved non-hydrogen angles: 1866 Unresolved non-hydrogen dihedrals: 1252 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 33, 'HIS:plan': 13, 'PHE:plan': 8, 'ASP:plan': 48, 'TYR:plan': 5, 'GLU:plan': 75, 'ARG:plan': 33, 'ASN:plan1': 24, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 970 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'T3X': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'T3X': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.80, per 1000 atoms: 0.24 Number of scatterers: 24222 At special positions: 0 Unit cell: (180.864, 120.105, 148.365, 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 140 16.00 P 4 15.00 F 6 9.00 O 4310 8.00 N 4154 7.00 C 15608 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: 2.18 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: 127 helices and 36 sheets defined 36.8% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'B' and resid 559 through 571 Processing helix chain 'B' and resid 585 through 596 removed outlier: 3.558A pdb=" N VAL B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 603 Processing helix chain 'B' and resid 604 through 607 Processing helix chain 'B' and resid 624 through 639 removed outlier: 3.814A pdb=" N ALA B 628 " --> pdb=" O GLY B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 659 removed outlier: 3.577A pdb=" N GLN B 645 " --> pdb=" O VAL B 641 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR B 646 " --> pdb=" O ALA B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 670 removed outlier: 3.635A pdb=" N LEU B 665 " --> pdb=" O SER B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 681 removed outlier: 3.971A pdb=" N HIS B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER B 681 " --> pdb=" O HIS B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 703 Processing helix chain 'B' and resid 705 through 719 Processing helix chain 'B' and resid 724 through 731 Processing helix chain 'B' and resid 743 through 751 removed outlier: 3.707A pdb=" N GLN B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) 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: 4.123A pdb=" N ARG B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 822 Processing helix chain 'B' and resid 834 through 853 Processing helix chain 'B' and resid 1004 through 1010 removed outlier: 3.696A pdb=" N VAL B1008 " --> pdb=" O CYS B1005 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B1010 " --> 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 removed outlier: 3.941A pdb=" N MET B1057 " --> pdb=" O LEU B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1240 through 1247 removed outlier: 4.327A pdb=" N ARG B1246 " --> pdb=" O LEU B1243 " (cutoff:3.500A) Processing helix chain 'B' and resid 1261 through 1267 removed outlier: 3.648A pdb=" N GLY B1265 " --> pdb=" O PRO B1262 " (cutoff:3.500A) Processing helix chain 'B' and resid 1285 through 1291 removed outlier: 3.556A pdb=" N MET B1288 " --> pdb=" O PRO B1285 " (cutoff:3.500A) Processing helix chain 'B' and resid 1314 through 1328 removed outlier: 3.706A pdb=" N LYS B1327 " --> pdb=" O GLN B1323 " (cutoff:3.500A) removed outlier: 3.590A 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 1409 removed outlier: 4.515A pdb=" N SER B1403 " --> pdb=" O GLU B1400 " (cutoff:3.500A) Proline residue: B1406 - end of helix removed outlier: 3.644A 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 1426 through 1431 Processing helix chain 'B' and resid 1431 through 1442 Processing helix chain 'B' and resid 1465 through 1473 removed outlier: 3.932A pdb=" N ILE B1469 " --> pdb=" O CYS B1465 " (cutoff:3.500A) 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 1590 through 1593 removed outlier: 4.234A pdb=" N SER B1593 " --> pdb=" O LEU B1590 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1590 through 1593' Processing helix chain 'B' and resid 1599 through 1610 removed outlier: 3.964A pdb=" N LEU B1603 " --> pdb=" O GLU B1599 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE B1610 " --> pdb=" O ILE B1606 " (cutoff:3.500A) Processing helix chain 'B' and resid 1611 through 1613 No H-bonds generated for 'chain 'B' and resid 1611 through 1613' Processing helix chain 'B' and resid 1645 through 1656 Processing helix chain 'B' and resid 1703 through 1712 removed outlier: 3.731A pdb=" N ARG B1707 " --> pdb=" O GLY B1703 " (cutoff:3.500A) Processing helix chain 'B' and resid 1770 through 1791 Processing helix chain 'B' and resid 1792 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 1871 through 1873 No H-bonds generated for 'chain 'B' and resid 1871 through 1873' Processing helix chain 'B' and resid 1881 through 1885 removed outlier: 3.746A pdb=" N LEU B1884 " --> pdb=" O PRO B1881 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B1885 " --> pdb=" O GLU B1882 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1881 through 1885' Processing helix chain 'B' and resid 1914 through 1926 removed outlier: 4.370A pdb=" N HIS B1926 " --> pdb=" O VAL B1922 " (cutoff:3.500A) Processing helix chain 'B' and resid 1954 through 1961 removed outlier: 3.829A pdb=" N LEU B1958 " --> pdb=" O SER B1954 " (cutoff:3.500A) 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 2035 through 2039 removed outlier: 4.153A pdb=" N ARG B2039 " --> pdb=" O PRO B2036 " (cutoff:3.500A) Processing helix chain 'B' and resid 2040 through 2045 Processing helix chain 'B' and resid 2052 through 2068 removed outlier: 4.063A pdb=" N VAL B2056 " --> pdb=" O GLN B2052 " (cutoff:3.500A) removed outlier: 3.856A 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 2124 through 2133 Processing helix chain 'B' and resid 2134 through 2139 removed outlier: 3.986A pdb=" N VAL B2138 " --> pdb=" O SER B2134 " (cutoff:3.500A) Processing helix chain 'B' and resid 2278 through 2282 removed outlier: 3.599A pdb=" N LYS B2281 " --> pdb=" O LYS B2278 " (cutoff:3.500A) Processing helix chain 'B' and resid 2308 through 2312 Processing helix chain 'B' and resid 2339 through 2343 removed outlier: 3.584A pdb=" N GLN B2342 " --> pdb=" O ARG B2339 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B2343 " --> pdb=" O THR B2340 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2339 through 2343' Processing helix chain 'B' and resid 2346 through 2351 Processing helix chain 'B' and resid 2389 through 2396 Processing helix chain 'B' and resid 2499 through 2526 Processing helix chain 'A' and resid 559 through 571 Processing helix chain 'A' and resid 585 through 596 removed outlier: 3.592A pdb=" N VAL A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 604 through 607 Processing helix chain 'A' and resid 624 through 639 removed outlier: 3.744A pdb=" N ALA A 628 " --> pdb=" O GLY A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 659 removed outlier: 3.617A pdb=" N GLN A 645 " --> pdb=" O VAL A 641 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR A 646 " --> pdb=" O ALA A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 670 removed outlier: 4.391A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 681 removed outlier: 4.054A pdb=" N HIS A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 703 Processing helix chain 'A' and resid 705 through 719 removed outlier: 3.524A pdb=" N LYS A 709 " --> pdb=" O ASP A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 731 Processing helix chain 'A' and resid 743 through 751 removed outlier: 3.749A pdb=" N GLN A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 764 Processing helix chain 'A' and resid 767 through 781 Processing helix chain 'A' and resid 783 through 795 removed outlier: 4.226A pdb=" N ARG A 793 " --> pdb=" O LEU A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 822 Processing helix chain 'A' and resid 834 through 853 Processing helix chain 'A' and resid 998 through 1002 Processing helix chain 'A' and resid 1004 through 1010 removed outlier: 3.542A pdb=" N VAL A1008 " --> pdb=" O CYS A1005 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A1010 " --> pdb=" O SER A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1051 through 1057 removed outlier: 3.936A pdb=" N MET A1057 " --> pdb=" O LEU A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1247 removed outlier: 4.335A pdb=" N ARG A1246 " --> pdb=" O LEU A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1267 removed outlier: 3.669A pdb=" N GLY A1265 " --> pdb=" O PRO A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1291 removed outlier: 3.546A pdb=" N MET A1288 " --> pdb=" O PRO A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1328 removed outlier: 3.878A pdb=" N LYS A1327 " --> pdb=" O GLN A1323 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A1328 " --> pdb=" O GLN A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1355 Processing helix chain 'A' and resid 1398 through 1409 removed outlier: 4.530A pdb=" N SER A1403 " --> pdb=" O GLU A1400 " (cutoff:3.500A) Proline residue: A1406 - end of helix removed outlier: 3.637A pdb=" N MET A1409 " --> pdb=" O PRO A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1424 Processing helix chain 'A' and resid 1426 through 1431 Processing helix chain 'A' and resid 1431 through 1442 Processing helix chain 'A' and resid 1465 through 1473 removed outlier: 3.992A pdb=" N ILE A1469 " --> pdb=" O CYS A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1510 Processing helix chain 'A' and resid 1517 through 1520 Processing helix chain 'A' and resid 1525 through 1538 Processing helix chain 'A' and resid 1550 through 1560 Processing helix chain 'A' and resid 1568 through 1579 Processing helix chain 'A' and resid 1590 through 1593 removed outlier: 4.232A pdb=" N SER A1593 " --> pdb=" O LEU A1590 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1590 through 1593' Processing helix chain 'A' and resid 1599 through 1610 removed outlier: 3.976A pdb=" N LEU A1603 " --> pdb=" O GLU A1599 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE A1610 " --> pdb=" O ILE A1606 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1613 No H-bonds generated for 'chain 'A' and resid 1611 through 1613' Processing helix chain 'A' and resid 1645 through 1656 Processing helix chain 'A' and resid 1703 through 1712 removed outlier: 3.782A pdb=" N ARG A1707 " --> pdb=" O GLY A1703 " (cutoff:3.500A) Processing helix chain 'A' and resid 1770 through 1791 Processing helix chain 'A' and resid 1792 through 1796 Processing helix chain 'A' and resid 1829 through 1834 Processing helix chain 'A' and resid 1853 through 1855 No H-bonds generated for 'chain 'A' and resid 1853 through 1855' Processing helix chain 'A' and resid 1871 through 1873 No H-bonds generated for 'chain 'A' and resid 1871 through 1873' Processing helix chain 'A' and resid 1881 through 1885 removed outlier: 3.752A pdb=" N LEU A1884 " --> pdb=" O PRO A1881 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A1885 " --> pdb=" O GLU A1882 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1881 through 1885' Processing helix chain 'A' and resid 1914 through 1926 removed outlier: 4.283A pdb=" N HIS A1926 " --> pdb=" O VAL A1922 " (cutoff:3.500A) Processing helix chain 'A' and resid 1954 through 1961 removed outlier: 3.887A pdb=" N LEU A1958 " --> pdb=" O SER A1954 " (cutoff:3.500A) Processing helix chain 'A' and resid 1967 through 1988 Processing helix chain 'A' and resid 1996 through 1998 No H-bonds generated for 'chain 'A' and resid 1996 through 1998' Processing helix chain 'A' and resid 2035 through 2039 removed outlier: 4.146A pdb=" N ARG A2039 " --> pdb=" O PRO A2036 " (cutoff:3.500A) Processing helix chain 'A' and resid 2040 through 2045 Processing helix chain 'A' and resid 2052 through 2068 removed outlier: 4.146A pdb=" N VAL A2056 " --> pdb=" O GLN A2052 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR A2057 " --> pdb=" O GLN A2053 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2099 Processing helix chain 'A' and resid 2104 through 2115 removed outlier: 3.515A pdb=" N GLU A2108 " --> pdb=" O TRP A2104 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2133 Processing helix chain 'A' and resid 2134 through 2139 removed outlier: 4.034A pdb=" N VAL A2138 " --> pdb=" O SER A2134 " (cutoff:3.500A) Processing helix chain 'A' and resid 2278 through 2282 removed outlier: 3.602A pdb=" N LYS A2281 " --> pdb=" O LYS A2278 " (cutoff:3.500A) Processing helix chain 'A' and resid 2308 through 2312 Processing helix chain 'A' and resid 2339 through 2343 removed outlier: 3.577A pdb=" N GLN A2342 " --> pdb=" O ARG A2339 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A2343 " --> pdb=" O THR A2340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2339 through 2343' Processing helix chain 'A' and resid 2346 through 2351 Processing helix chain 'A' and resid 2389 through 2396 Processing helix chain 'A' and resid 2499 through 2526 Processing sheet with id=AA1, first strand: chain 'B' and resid 796 through 797 removed outlier: 6.511A pdb=" N ILE B 803 " --> pdb=" O ASP B 988 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU B1063 " --> pdb=" O ASN B1089 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU B1134 " --> pdb=" O SER B1159 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE B1158 " --> pdb=" O LYS B1179 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU B1178 " --> pdb=" O ASP B1202 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU B1201 " --> pdb=" O LEU B1226 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU B1225 " --> pdb=" O HIS B1251 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU B1250 " --> pdb=" O ASP B1274 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 1329 through 1332 removed outlier: 4.356A pdb=" N GLN B1521 " --> pdb=" O TYR B1332 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 1376 through 1378 removed outlier: 9.361A pdb=" N LEU B1414 " --> pdb=" O ARG B1334 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS B1336 " --> pdb=" O LEU B1414 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU B1416 " --> pdb=" O LYS B1336 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N MET B1338 " --> pdb=" O LEU B1416 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL B1418 " --> pdb=" O MET B1338 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL B1340 " --> pdb=" O VAL B1418 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N ILE B1448 " --> pdb=" O ALA B1413 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR B1415 " --> pdb=" O ILE B1448 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL B1450 " --> pdb=" O TYR B1415 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ALA B1417 " --> pdb=" O VAL B1450 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL B1447 " --> pdb=" O ARG B1483 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1547 through 1549 Processing sheet with id=AA5, first strand: chain 'B' and resid 1679 through 1681 removed outlier: 3.663A pdb=" N VAL B1679 " --> pdb=" O TYR A1733 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A1731 " --> pdb=" O GLU B1681 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1690 through 1691 Processing sheet with id=AA7, first strand: chain 'B' and resid 1695 through 1696 Processing sheet with id=AA8, first strand: chain 'B' and resid 1740 through 1741 removed outlier: 3.701A pdb=" N ARG B1731 " --> pdb=" O GLU A1681 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A1679 " --> pdb=" O TYR B1733 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1840 through 1841 Processing sheet with id=AB1, first strand: chain 'B' and resid 1875 through 1876 removed outlier: 3.998A pdb=" N ALA B1897 " --> pdb=" O GLU B1876 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLU B1948 " --> pdb=" O LEU B1935 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU B1935 " --> pdb=" O GLU B1948 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 2000 through 2002 Processing sheet with id=AB3, first strand: chain 'B' and resid 2140 through 2146 removed outlier: 6.675A pdb=" N VAL B2495 " --> pdb=" O THR B2141 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG B2143 " --> pdb=" O LEU B2493 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU B2493 " --> pdb=" O ARG B2143 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU B2145 " --> pdb=" O SER B2491 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N SER B2491 " --> pdb=" O LEU B2145 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL B2469 " --> pdb=" O THR B2460 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N THR B2460 " --> pdb=" O VAL B2469 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU B2471 " --> pdb=" O MET B2458 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N MET B2458 " --> pdb=" O LEU B2471 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU B2473 " --> pdb=" O ARG B2456 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 2152 through 2154 Processing sheet with id=AB5, first strand: chain 'B' and resid 2166 through 2167 Processing sheet with id=AB6, first strand: chain 'B' and resid 2199 through 2207 removed outlier: 4.862A pdb=" N CYS B2201 " --> pdb=" O GLY B2218 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY B2218 " --> pdb=" O CYS B2201 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B2215 " --> pdb=" O ILE B2227 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 2247 through 2251 Processing sheet with id=AB8, first strand: chain 'B' and resid 2304 through 2305 removed outlier: 6.435A pdb=" N ILE B2323 " --> pdb=" O LEU B2335 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU B2335 " --> pdb=" O ILE B2323 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N SER B2325 " --> pdb=" O GLN B2333 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 2354 through 2359 removed outlier: 6.968A pdb=" N ALA B2366 " --> pdb=" O ILE B2355 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL B2357 " --> pdb=" O TYR B2364 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR B2364 " --> pdb=" O VAL B2357 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL B2359 " --> pdb=" O ALA B2362 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA B2362 " --> pdb=" O VAL B2359 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS B2367 " --> pdb=" O VAL B2372 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B2372 " --> pdb=" O LYS B2367 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ASP B2377 " --> pdb=" O LEU B2383 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B2383 " --> pdb=" O ASP B2377 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 2414 through 2420 removed outlier: 6.877A pdb=" N GLY B2428 " --> pdb=" O LYS B2415 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU B2417 " --> pdb=" O TRP B2426 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N TRP B2426 " --> pdb=" O LEU B2417 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU B2419 " --> pdb=" O ALA B2424 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ALA B2424 " --> pdb=" O LEU B2419 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG B2446 " --> pdb=" O LEU B2436 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASP B2438 " --> pdb=" O LEU B2444 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU B2444 " --> pdb=" O ASP B2438 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 796 through 797 removed outlier: 6.517A pdb=" N ILE A 803 " --> pdb=" O ASP A 988 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU A1063 " --> pdb=" O ASN A1089 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE A1158 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU A1178 " --> pdb=" O ASP A1202 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU A1201 " --> pdb=" O LEU A1226 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A1225 " --> pdb=" O HIS A1251 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU A1250 " --> pdb=" O ASP A1274 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1329 through 1332 removed outlier: 4.340A pdb=" N GLN A1521 " --> pdb=" O TYR A1332 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1376 through 1378 removed outlier: 3.519A pdb=" N MET A1335 " --> pdb=" O VAL A1389 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N LEU A1414 " --> pdb=" O ARG A1334 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS A1336 " --> pdb=" O LEU A1414 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU A1416 " --> pdb=" O LYS A1336 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N MET A1338 " --> pdb=" O LEU A1416 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL A1418 " --> pdb=" O MET A1338 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A1340 " --> pdb=" O VAL A1418 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N ILE A1448 " --> pdb=" O ALA A1413 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N TYR A1415 " --> pdb=" O ILE A1448 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL A1450 " --> pdb=" O TYR A1415 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ALA A1417 " --> pdb=" O VAL A1450 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL A1447 " --> pdb=" O ARG A1483 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1547 through 1549 Processing sheet with id=AC6, first strand: chain 'A' and resid 1690 through 1691 Processing sheet with id=AC7, first strand: chain 'A' and resid 1695 through 1696 Processing sheet with id=AC8, first strand: chain 'A' and resid 1840 through 1841 Processing sheet with id=AC9, first strand: chain 'A' and resid 1875 through 1876 removed outlier: 3.980A pdb=" N ALA A1897 " --> pdb=" O GLU A1876 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU A1948 " --> pdb=" O LEU A1935 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU A1935 " --> pdb=" O GLU A1948 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 2000 through 2002 Processing sheet with id=AD2, first strand: chain 'A' and resid 2140 through 2146 removed outlier: 6.593A pdb=" N LEU A2140 " --> pdb=" O ASP A2497 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASP A2497 " --> pdb=" O LEU A2140 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N SER A2491 " --> pdb=" O LEU A2146 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL A2469 " --> pdb=" O THR A2460 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N THR A2460 " --> pdb=" O VAL A2469 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A2471 " --> pdb=" O MET A2458 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET A2458 " --> pdb=" O LEU A2471 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU A2473 " --> pdb=" O ARG A2456 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 2166 through 2167 Processing sheet with id=AD4, first strand: chain 'A' and resid 2170 through 2171 Processing sheet with id=AD5, first strand: chain 'A' and resid 2199 through 2207 removed outlier: 4.868A pdb=" N CYS A2201 " --> pdb=" O GLY A2218 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY A2218 " --> pdb=" O CYS A2201 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A2215 " --> pdb=" O ILE A2227 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 2247 through 2251 Processing sheet with id=AD7, first strand: chain 'A' and resid 2304 through 2305 removed outlier: 6.376A pdb=" N ILE A2323 " --> pdb=" O LEU A2335 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU A2335 " --> pdb=" O ILE A2323 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N SER A2325 " --> pdb=" O GLN A2333 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 2354 through 2359 removed outlier: 6.969A pdb=" N ALA A2366 " --> pdb=" O ILE A2355 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL A2357 " --> pdb=" O TYR A2364 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR A2364 " --> pdb=" O VAL A2357 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N VAL A2359 " --> pdb=" O ALA A2362 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA A2362 " --> pdb=" O VAL A2359 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASP A2377 " --> pdb=" O LEU A2383 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A2383 " --> pdb=" O ASP A2377 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 2414 through 2420 removed outlier: 6.865A pdb=" N GLY A2428 " --> pdb=" O LYS A2415 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU A2417 " --> pdb=" O TRP A2426 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N TRP A2426 " --> pdb=" O LEU A2417 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LEU A2419 " --> pdb=" O ALA A2424 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ALA A2424 " --> pdb=" O LEU A2419 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG A2446 " --> pdb=" O LEU A2436 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ASP A2438 " --> pdb=" O LEU A2444 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A2444 " --> pdb=" O ASP A2438 " (cutoff:3.500A) 966 hydrogen bonds defined for protein. 2571 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: 6.34 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3868 1.31 - 1.44: 6172 1.44 - 1.56: 14430 1.56 - 1.69: 6 1.69 - 1.81: 200 Bond restraints: 24676 Sorted by residual: bond pdb=" C17 T3X B2602 " pdb=" N18 T3X B2602 " ideal model delta sigma weight residual 1.456 1.267 0.189 2.00e-02 2.50e+03 8.94e+01 bond pdb=" C17 T3X A2602 " pdb=" N18 T3X A2602 " ideal model delta sigma weight residual 1.456 1.267 0.189 2.00e-02 2.50e+03 8.89e+01 bond pdb=" C24 T3X B2602 " pdb=" N21 T3X B2602 " ideal model delta sigma weight residual 1.451 1.266 0.185 2.00e-02 2.50e+03 8.56e+01 bond pdb=" C24 T3X A2602 " pdb=" N21 T3X A2602 " ideal model delta sigma weight residual 1.451 1.267 0.184 2.00e-02 2.50e+03 8.49e+01 bond pdb=" C30 T3X A2602 " pdb=" C31 T3X A2602 " ideal model delta sigma weight residual 1.419 1.541 -0.122 2.00e-02 2.50e+03 3.74e+01 ... (remaining 24671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 32966 1.94 - 3.87: 689 3.87 - 5.81: 104 5.81 - 7.74: 18 7.74 - 9.68: 3 Bond angle restraints: 33780 Sorted by residual: angle pdb=" CG1 ILE A 997 " pdb=" CB ILE A 997 " pdb=" CG2 ILE A 997 " ideal model delta sigma weight residual 110.70 101.02 9.68 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C08 T3X B2602 " pdb=" N10 T3X B2602 " pdb=" C11 T3X B2602 " ideal model delta sigma weight residual 129.30 120.76 8.54 3.00e+00 1.11e-01 8.10e+00 angle pdb=" C08 T3X A2602 " pdb=" N10 T3X A2602 " pdb=" C11 T3X A2602 " ideal model delta sigma weight residual 129.30 120.80 8.50 3.00e+00 1.11e-01 8.04e+00 angle pdb=" N LYS A1184 " pdb=" CA LYS A1184 " pdb=" C LYS A1184 " ideal model delta sigma weight residual 109.71 113.43 -3.72 1.41e+00 5.03e-01 6.98e+00 angle pdb=" C GLU A1805 " pdb=" N THR A1806 " pdb=" CA THR A1806 " ideal model delta sigma weight residual 121.54 126.57 -5.03 1.91e+00 2.74e-01 6.93e+00 ... (remaining 33775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.84: 14174 23.84 - 47.68: 500 47.68 - 71.52: 30 71.52 - 95.36: 13 95.36 - 119.21: 5 Dihedral angle restraints: 14722 sinusoidal: 4760 harmonic: 9962 Sorted by residual: dihedral pdb=" O2B GDP A2601 " pdb=" O3A GDP A2601 " pdb=" PB GDP A2601 " pdb=" PA GDP A2601 " ideal model delta sinusoidal sigma weight residual -180.00 -64.25 -115.75 1 2.00e+01 2.50e-03 3.44e+01 dihedral pdb=" O2B GDP B2601 " pdb=" O3A GDP B2601 " pdb=" PB GDP B2601 " pdb=" PA GDP B2601 " ideal model delta sinusoidal sigma weight residual -180.00 -64.34 -115.66 1 2.00e+01 2.50e-03 3.44e+01 dihedral pdb=" CA PRO B 597 " pdb=" C PRO B 597 " pdb=" N ASP B 598 " pdb=" CA ASP B 598 " ideal model delta harmonic sigma weight residual -180.00 -156.82 -23.18 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 14719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3408 0.057 - 0.113: 697 0.113 - 0.170: 117 0.170 - 0.226: 1 0.226 - 0.283: 3 Chirality restraints: 4226 Sorted by residual: chirality pdb=" CA GLN B1182 " pdb=" N GLN B1182 " pdb=" C GLN B1182 " pdb=" CB GLN B1182 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA GLN A1182 " pdb=" N GLN A1182 " pdb=" C GLN A1182 " pdb=" CB GLN A1182 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE A 997 " pdb=" CA ILE A 997 " pdb=" CG1 ILE A 997 " pdb=" CG2 ILE A 997 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 4223 not shown) Planarity restraints: 4230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B2104 " 0.026 2.00e-02 2.50e+03 1.84e-02 8.51e+00 pdb=" CG TRP B2104 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP B2104 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B2104 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B2104 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B2104 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B2104 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B2104 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B2104 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B2104 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1763 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.51e+00 pdb=" C LEU A1763 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU A1763 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS A1764 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B1763 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.33e+00 pdb=" C LEU B1763 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU B1763 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS B1764 " 0.014 2.00e-02 2.50e+03 ... (remaining 4227 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3780 2.76 - 3.30: 23979 3.30 - 3.83: 38405 3.83 - 4.37: 43646 4.37 - 4.90: 75455 Nonbonded interactions: 185265 Sorted by model distance: nonbonded pdb=" O VAL A 748 " pdb=" OG SER A 753 " model vdw 2.231 3.040 nonbonded pdb=" O VAL B 748 " pdb=" OG SER B 753 " model vdw 2.231 3.040 nonbonded pdb=" OG SER A2166 " pdb=" O LEU A2182 " model vdw 2.235 3.040 nonbonded pdb=" OG SER B2166 " pdb=" O LEU B2182 " model vdw 2.252 3.040 nonbonded pdb=" O HIS B 677 " pdb=" OG SER B 681 " model vdw 2.267 3.040 ... (remaining 185260 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: 0.05 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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 group one per residue 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: 3.310 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.520 Find NCS groups from input model: 0.300 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: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 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 : 0.005 0.189 24676 Z= 0.234 Angle : 0.696 9.681 33780 Z= 0.355 Chirality : 0.047 0.283 4226 Planarity : 0.004 0.042 4230 Dihedral : 12.703 119.205 8214 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % 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: -2.91 (0.13), residues: 3346 helix: -1.29 (0.14), residues: 1058 sheet: -2.13 (0.20), residues: 658 loop : -2.23 (0.14), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B2235 TYR 0.013 0.001 TYR B1419 PHE 0.015 0.002 PHE B1148 TRP 0.049 0.002 TRP B2104 HIS 0.012 0.001 HIS B1043 Details of bonding type rmsd covalent geometry : bond 0.00486 (24676) covalent geometry : angle 0.69587 (33780) hydrogen bonds : bond 0.20739 ( 966) hydrogen bonds : angle 7.19440 ( 2571) *********************** 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 316 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1168 MET cc_start: 0.6984 (tpp) cc_final: 0.6619 (tpp) REVERT: B 1288 MET cc_start: 0.8769 (ttm) cc_final: 0.8422 (ttp) REVERT: A 1372 ASP cc_start: 0.5287 (t0) cc_final: 0.3510 (m-30) REVERT: A 2136 GLU cc_start: 0.7526 (mp0) cc_final: 0.6515 (tm-30) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.1498 time to fit residues: 76.9446 Evaluate side-chains 138 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1045 ASN ** B1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1971 GLN ** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.113974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.084894 restraints weight = 73678.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.087715 restraints weight = 37361.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.089532 restraints weight = 24665.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.090659 restraints weight = 18939.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.091443 restraints weight = 15980.449| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24676 Z= 0.148 Angle : 0.627 9.560 33780 Z= 0.316 Chirality : 0.043 0.202 4226 Planarity : 0.004 0.040 4230 Dihedral : 6.653 110.209 3614 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.32 % Allowed : 10.88 % Favored : 87.80 % 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: -1.59 (0.14), residues: 3346 helix: 0.26 (0.16), residues: 1080 sheet: -1.76 (0.20), residues: 650 loop : -1.64 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2339 TYR 0.018 0.001 TYR A1402 PHE 0.015 0.001 PHE A1148 TRP 0.039 0.002 TRP A1376 HIS 0.007 0.001 HIS B2510 Details of bonding type rmsd covalent geometry : bond 0.00338 (24676) covalent geometry : angle 0.62738 (33780) hydrogen bonds : bond 0.04048 ( 966) hydrogen bonds : angle 5.11273 ( 2571) *********************** 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 185 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1351 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7480 (tp) REVERT: A 1944 MET cc_start: 0.8286 (ptp) cc_final: 0.8071 (ptp) REVERT: A 2240 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7645 (mmmt) REVERT: A 2393 LEU cc_start: 0.7091 (mm) cc_final: 0.5642 (pp) REVERT: A 2458 MET cc_start: 0.6180 (ptm) cc_final: 0.5862 (ptm) outliers start: 30 outliers final: 18 residues processed: 182 average time/residue: 0.1484 time to fit residues: 45.9733 Evaluate side-chains 147 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 1340 VAL Chi-restraints excluded: chain B residue 1584 HIS Chi-restraints excluded: chain B residue 1750 VAL Chi-restraints excluded: chain B residue 1752 SER Chi-restraints excluded: chain B residue 1935 LEU Chi-restraints excluded: chain B residue 2167 ILE Chi-restraints excluded: chain B residue 2248 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 1021 ASN Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1485 TYR Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1584 HIS Chi-restraints excluded: chain A residue 2240 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 297 optimal weight: 0.0270 chunk 258 optimal weight: 2.9990 chunk 273 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 171 optimal weight: 30.0000 chunk 223 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 332 optimal weight: 4.9990 chunk 150 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 overall best weight: 1.0840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 992 ASN ** B1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1425 GLN B1872 ASN B2008 ASN A 693 ASN ** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1730 ASN A1872 ASN A2490 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.111782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.082019 restraints weight = 75109.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.085706 restraints weight = 41083.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.086270 restraints weight = 25352.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.087057 restraints weight = 20555.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.087427 restraints weight = 19333.285| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24676 Z= 0.153 Angle : 0.601 7.917 33780 Z= 0.302 Chirality : 0.043 0.165 4226 Planarity : 0.003 0.039 4230 Dihedral : 6.508 113.239 3614 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.29 % Allowed : 13.48 % Favored : 84.23 % 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: -0.97 (0.15), residues: 3346 helix: 0.92 (0.17), residues: 1060 sheet: -1.52 (0.21), residues: 634 loop : -1.29 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B2456 TYR 0.023 0.001 TYR B2475 PHE 0.017 0.001 PHE B1479 TRP 0.048 0.002 TRP A1376 HIS 0.007 0.001 HIS A1043 Details of bonding type rmsd covalent geometry : bond 0.00349 (24676) covalent geometry : angle 0.60096 (33780) hydrogen bonds : bond 0.03628 ( 966) hydrogen bonds : angle 4.60304 ( 2571) *********************** 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 189 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 992 ASN cc_start: 0.7424 (OUTLIER) cc_final: 0.7159 (t0) REVERT: B 1168 MET cc_start: 0.7387 (tpp) cc_final: 0.6952 (tpp) REVERT: B 1509 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8486 (mp) REVERT: B 2104 TRP cc_start: 0.9100 (OUTLIER) cc_final: 0.8370 (t60) REVERT: B 2137 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7347 (mp) REVERT: A 2393 LEU cc_start: 0.7160 (mm) cc_final: 0.5758 (pp) outliers start: 52 outliers final: 29 residues processed: 185 average time/residue: 0.1348 time to fit residues: 43.7239 Evaluate side-chains 154 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 992 ASN Chi-restraints excluded: chain B residue 1049 SER Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1326 LEU Chi-restraints excluded: chain B residue 1340 VAL Chi-restraints excluded: chain B residue 1373 VAL Chi-restraints excluded: chain B residue 1509 LEU Chi-restraints excluded: chain B residue 1584 HIS Chi-restraints excluded: chain B residue 1750 VAL Chi-restraints excluded: chain B residue 1752 SER Chi-restraints excluded: chain B residue 1935 LEU Chi-restraints excluded: chain B residue 2008 ASN Chi-restraints excluded: chain B residue 2104 TRP Chi-restraints excluded: chain B residue 2111 ILE Chi-restraints excluded: chain B residue 2137 LEU Chi-restraints excluded: chain B residue 2167 ILE Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1485 TYR Chi-restraints excluded: chain A residue 1584 HIS Chi-restraints excluded: chain A residue 2202 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 212 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 272 optimal weight: 0.9980 chunk 273 optimal weight: 0.7980 chunk 229 optimal weight: 0.0670 chunk 204 optimal weight: 0.3980 chunk 187 optimal weight: 4.9990 chunk 72 optimal weight: 0.0870 chunk 1 optimal weight: 0.3980 chunk 326 optimal weight: 0.9990 chunk 240 optimal weight: 1.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 693 ASN ** B1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1333 ASN B1730 ASN B2008 ASN A1039 HIS ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.110817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.081577 restraints weight = 76016.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.084811 restraints weight = 44185.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.085431 restraints weight = 26572.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.085776 restraints weight = 25517.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.086005 restraints weight = 22807.119| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24676 Z= 0.097 Angle : 0.543 7.857 33780 Z= 0.273 Chirality : 0.042 0.161 4226 Planarity : 0.003 0.036 4230 Dihedral : 6.169 110.899 3614 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.67 % Allowed : 14.80 % Favored : 83.52 % 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: -0.73 (0.15), residues: 3346 helix: 1.15 (0.17), residues: 1060 sheet: -1.40 (0.21), residues: 630 loop : -1.17 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1957 TYR 0.015 0.001 TYR B2475 PHE 0.014 0.001 PHE B1883 TRP 0.036 0.001 TRP A1376 HIS 0.007 0.001 HIS B1043 Details of bonding type rmsd covalent geometry : bond 0.00215 (24676) covalent geometry : angle 0.54271 (33780) hydrogen bonds : bond 0.03070 ( 966) hydrogen bonds : angle 4.40721 ( 2571) *********************** 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 172 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1185 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6213 (m-80) REVERT: B 1509 LEU cc_start: 0.8786 (tt) cc_final: 0.8439 (mp) REVERT: B 2104 TRP cc_start: 0.9099 (OUTLIER) cc_final: 0.8526 (t60) REVERT: B 2137 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7231 (mp) REVERT: A 712 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8164 (mpp) REVERT: A 2393 LEU cc_start: 0.7030 (mm) cc_final: 0.5677 (pp) outliers start: 38 outliers final: 23 residues processed: 166 average time/residue: 0.1352 time to fit residues: 39.8192 Evaluate side-chains 152 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 1185 PHE Chi-restraints excluded: chain B residue 1326 LEU Chi-restraints excluded: chain B residue 1340 VAL Chi-restraints excluded: chain B residue 1470 THR Chi-restraints excluded: chain B residue 1584 HIS Chi-restraints excluded: chain B residue 1750 VAL Chi-restraints excluded: chain B residue 1861 LEU Chi-restraints excluded: chain B residue 1935 LEU Chi-restraints excluded: chain B residue 2008 ASN Chi-restraints excluded: chain B residue 2104 TRP Chi-restraints excluded: chain B residue 2137 LEU Chi-restraints excluded: chain B residue 2167 ILE Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1485 TYR Chi-restraints excluded: chain A residue 1584 HIS Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 2202 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 89 optimal weight: 4.9990 chunk 76 optimal weight: 0.0570 chunk 80 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 129 optimal weight: 0.7980 chunk 234 optimal weight: 1.9990 chunk 256 optimal weight: 0.1980 chunk 73 optimal weight: 0.9990 chunk 192 optimal weight: 0.7980 chunk 284 optimal weight: 1.9990 chunk 326 optimal weight: 9.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1730 ASN ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.110625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.084671 restraints weight = 75601.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.083961 restraints weight = 43365.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.084494 restraints weight = 37131.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.084983 restraints weight = 31740.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.085279 restraints weight = 27569.428| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24676 Z= 0.097 Angle : 0.543 7.856 33780 Z= 0.273 Chirality : 0.042 0.160 4226 Planarity : 0.003 0.036 4230 Dihedral : 6.200 110.899 3614 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.19 % Allowed : 15.37 % Favored : 83.44 % 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: -0.73 (0.15), residues: 3346 helix: 1.15 (0.17), residues: 1060 sheet: -1.40 (0.21), residues: 630 loop : -1.17 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1957 TYR 0.015 0.001 TYR B2475 PHE 0.014 0.001 PHE B1883 TRP 0.036 0.001 TRP A1376 HIS 0.007 0.001 HIS B1043 Details of bonding type rmsd covalent geometry : bond 0.00215 (24676) covalent geometry : angle 0.54267 (33780) hydrogen bonds : bond 0.03070 ( 966) hydrogen bonds : angle 4.40723 ( 2571) *********************** 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 152 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1185 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6347 (m-80) REVERT: B 1509 LEU cc_start: 0.8789 (tt) cc_final: 0.8443 (mp) REVERT: B 2104 TRP cc_start: 0.9090 (OUTLIER) cc_final: 0.8523 (t60) REVERT: B 2137 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7258 (mp) REVERT: A 712 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8144 (mpp) REVERT: A 2393 LEU cc_start: 0.6950 (mm) cc_final: 0.5603 (pp) outliers start: 27 outliers final: 23 residues processed: 149 average time/residue: 0.1369 time to fit residues: 36.1152 Evaluate side-chains 151 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 1185 PHE Chi-restraints excluded: chain B residue 1326 LEU Chi-restraints excluded: chain B residue 1340 VAL Chi-restraints excluded: chain B residue 1470 THR Chi-restraints excluded: chain B residue 1584 HIS Chi-restraints excluded: chain B residue 1750 VAL Chi-restraints excluded: chain B residue 1861 LEU Chi-restraints excluded: chain B residue 1935 LEU Chi-restraints excluded: chain B residue 2008 ASN Chi-restraints excluded: chain B residue 2104 TRP Chi-restraints excluded: chain B residue 2137 LEU Chi-restraints excluded: chain B residue 2167 ILE Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1485 TYR Chi-restraints excluded: chain A residue 1584 HIS Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 2202 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 21 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 174 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 chunk 142 optimal weight: 20.0000 chunk 211 optimal weight: 0.5980 chunk 120 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1730 ASN ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.110559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.080883 restraints weight = 75945.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.084039 restraints weight = 44236.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.084916 restraints weight = 26777.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.085484 restraints weight = 24454.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.085723 restraints weight = 22560.969| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24676 Z= 0.098 Angle : 0.543 7.848 33780 Z= 0.273 Chirality : 0.042 0.157 4226 Planarity : 0.003 0.036 4230 Dihedral : 6.201 110.898 3614 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.19 % Allowed : 15.42 % Favored : 83.39 % 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: -0.73 (0.15), residues: 3346 helix: 1.16 (0.17), residues: 1060 sheet: -1.40 (0.21), residues: 630 loop : -1.17 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1957 TYR 0.015 0.001 TYR B2475 PHE 0.014 0.001 PHE B1883 TRP 0.036 0.001 TRP A1376 HIS 0.007 0.001 HIS B1043 Details of bonding type rmsd covalent geometry : bond 0.00217 (24676) covalent geometry : angle 0.54251 (33780) hydrogen bonds : bond 0.03072 ( 966) hydrogen bonds : angle 4.40737 ( 2571) *********************** 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 151 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1185 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.6236 (m-80) REVERT: B 1509 LEU cc_start: 0.8802 (tt) cc_final: 0.8447 (mp) REVERT: B 2104 TRP cc_start: 0.9097 (OUTLIER) cc_final: 0.8533 (t60) REVERT: B 2137 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7241 (mp) REVERT: A 712 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8164 (mpp) REVERT: A 2393 LEU cc_start: 0.7033 (mm) cc_final: 0.5678 (pp) outliers start: 27 outliers final: 23 residues processed: 148 average time/residue: 0.1388 time to fit residues: 36.0053 Evaluate side-chains 151 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 1185 PHE Chi-restraints excluded: chain B residue 1326 LEU Chi-restraints excluded: chain B residue 1340 VAL Chi-restraints excluded: chain B residue 1470 THR Chi-restraints excluded: chain B residue 1584 HIS Chi-restraints excluded: chain B residue 1750 VAL Chi-restraints excluded: chain B residue 1861 LEU Chi-restraints excluded: chain B residue 1935 LEU Chi-restraints excluded: chain B residue 2008 ASN Chi-restraints excluded: chain B residue 2104 TRP Chi-restraints excluded: chain B residue 2137 LEU Chi-restraints excluded: chain B residue 2167 ILE Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1485 TYR Chi-restraints excluded: chain A residue 1584 HIS Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 2202 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 93 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 60 optimal weight: 0.0870 chunk 143 optimal weight: 0.0770 chunk 221 optimal weight: 0.0970 chunk 126 optimal weight: 0.0970 chunk 292 optimal weight: 1.9990 chunk 164 optimal weight: 0.0970 chunk 330 optimal weight: 3.9990 chunk 279 optimal weight: 0.7980 overall best weight: 0.0910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2008 ASN ** B2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.111585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.082219 restraints weight = 75509.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.084774 restraints weight = 40432.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.086474 restraints weight = 27591.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.087554 restraints weight = 21590.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.088284 restraints weight = 18376.574| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24676 Z= 0.091 Angle : 0.532 8.478 33780 Z= 0.265 Chirality : 0.041 0.200 4226 Planarity : 0.003 0.040 4230 Dihedral : 5.950 110.890 3614 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.63 % Allowed : 15.33 % Favored : 83.04 % 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: -0.55 (0.15), residues: 3346 helix: 1.33 (0.17), residues: 1064 sheet: -1.30 (0.22), residues: 614 loop : -1.10 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B2122 TYR 0.013 0.001 TYR B2475 PHE 0.014 0.001 PHE B1883 TRP 0.024 0.001 TRP B2104 HIS 0.007 0.001 HIS B1043 Details of bonding type rmsd covalent geometry : bond 0.00198 (24676) covalent geometry : angle 0.53182 (33780) hydrogen bonds : bond 0.02780 ( 966) hydrogen bonds : angle 4.22766 ( 2571) *********************** 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 172 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1185 PHE cc_start: 0.6912 (OUTLIER) cc_final: 0.6063 (m-80) REVERT: B 2137 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7086 (mp) REVERT: B 2301 MET cc_start: 0.3044 (mtm) cc_final: 0.2447 (ptp) REVERT: A 712 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8127 (mpp) REVERT: A 2301 MET cc_start: 0.4089 (mpp) cc_final: 0.3860 (mpp) REVERT: A 2393 LEU cc_start: 0.6732 (mm) cc_final: 0.5515 (pp) outliers start: 37 outliers final: 22 residues processed: 164 average time/residue: 0.1382 time to fit residues: 39.5813 Evaluate side-chains 150 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1185 PHE Chi-restraints excluded: chain B residue 1288 MET Chi-restraints excluded: chain B residue 1326 LEU Chi-restraints excluded: chain B residue 1470 THR Chi-restraints excluded: chain B residue 1750 VAL Chi-restraints excluded: chain B residue 1752 SER Chi-restraints excluded: chain B residue 1861 LEU Chi-restraints excluded: chain B residue 1935 LEU Chi-restraints excluded: chain B residue 2137 LEU Chi-restraints excluded: chain B residue 2167 ILE Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1485 TYR Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 2202 LEU Chi-restraints excluded: chain A residue 2458 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 66 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 262 optimal weight: 2.9990 chunk 271 optimal weight: 0.0570 chunk 242 optimal weight: 0.9980 chunk 186 optimal weight: 0.0870 chunk 126 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 chunk 162 optimal weight: 10.0000 chunk 319 optimal weight: 20.0000 chunk 289 optimal weight: 2.9990 overall best weight: 1.0278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 721 ASN ** B1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.109266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.078870 restraints weight = 75453.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.082155 restraints weight = 43482.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.082768 restraints weight = 28159.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.083433 restraints weight = 23043.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.083786 restraints weight = 21374.262| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24676 Z= 0.138 Angle : 0.571 8.584 33780 Z= 0.286 Chirality : 0.042 0.166 4226 Planarity : 0.003 0.036 4230 Dihedral : 5.967 107.943 3614 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.67 % Allowed : 15.20 % Favored : 83.13 % 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: -0.43 (0.15), residues: 3346 helix: 1.40 (0.17), residues: 1068 sheet: -1.27 (0.22), residues: 622 loop : -0.98 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A2122 TYR 0.014 0.001 TYR B1739 PHE 0.020 0.001 PHE A 671 TRP 0.025 0.002 TRP A1376 HIS 0.007 0.001 HIS A2510 Details of bonding type rmsd covalent geometry : bond 0.00321 (24676) covalent geometry : angle 0.57136 (33780) hydrogen bonds : bond 0.03131 ( 966) hydrogen bonds : angle 4.22107 ( 2571) *********************** 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 167 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1185 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.6419 (m-80) REVERT: B 2104 TRP cc_start: 0.9096 (OUTLIER) cc_final: 0.8514 (t60) REVERT: B 2137 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7489 (mp) REVERT: A 712 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8312 (mpp) REVERT: A 1099 PRO cc_start: 0.8432 (Cg_exo) cc_final: 0.8215 (Cg_endo) REVERT: A 2393 LEU cc_start: 0.6893 (mm) cc_final: 0.5612 (pp) outliers start: 38 outliers final: 28 residues processed: 156 average time/residue: 0.1441 time to fit residues: 38.4443 Evaluate side-chains 155 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain B residue 1185 PHE Chi-restraints excluded: chain B residue 1288 MET Chi-restraints excluded: chain B residue 1326 LEU Chi-restraints excluded: chain B residue 1470 THR Chi-restraints excluded: chain B residue 1750 VAL Chi-restraints excluded: chain B residue 1752 SER Chi-restraints excluded: chain B residue 1861 LEU Chi-restraints excluded: chain B residue 1935 LEU Chi-restraints excluded: chain B residue 2104 TRP Chi-restraints excluded: chain B residue 2115 LEU Chi-restraints excluded: chain B residue 2137 LEU Chi-restraints excluded: chain B residue 2167 ILE Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1185 PHE Chi-restraints excluded: chain A residue 1485 TYR Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1584 HIS Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 2202 LEU Chi-restraints excluded: chain A residue 2458 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 81 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 297 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 302 optimal weight: 0.7980 chunk 252 optimal weight: 0.0270 chunk 127 optimal weight: 0.0010 chunk 17 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 285 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 overall best weight: 0.9648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2173 HIS ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2008 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.109148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.078833 restraints weight = 75683.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.082559 restraints weight = 42190.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.083268 restraints weight = 24592.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.083675 restraints weight = 21935.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.083923 restraints weight = 20115.390| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24676 Z= 0.134 Angle : 0.581 11.428 33780 Z= 0.290 Chirality : 0.042 0.164 4226 Planarity : 0.003 0.037 4230 Dihedral : 5.895 108.411 3614 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.63 % Allowed : 15.86 % Favored : 82.51 % 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: -0.42 (0.15), residues: 3346 helix: 1.44 (0.17), residues: 1066 sheet: -1.28 (0.21), residues: 636 loop : -0.98 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1866 TYR 0.012 0.001 TYR B1402 PHE 0.015 0.001 PHE A1227 TRP 0.024 0.002 TRP A1376 HIS 0.007 0.001 HIS B1043 Details of bonding type rmsd covalent geometry : bond 0.00311 (24676) covalent geometry : angle 0.58075 (33780) hydrogen bonds : bond 0.03036 ( 966) hydrogen bonds : angle 4.22049 ( 2571) *********************** 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 162 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1185 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6540 (m-80) REVERT: B 2104 TRP cc_start: 0.9100 (OUTLIER) cc_final: 0.8524 (t60) REVERT: B 2137 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7487 (mp) REVERT: A 712 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8305 (mpp) REVERT: A 1057 MET cc_start: 0.6835 (mtm) cc_final: 0.6548 (mtt) REVERT: A 1099 PRO cc_start: 0.8427 (Cg_exo) cc_final: 0.8216 (Cg_endo) REVERT: A 1175 MET cc_start: 0.6059 (ptp) cc_final: 0.5646 (ptp) REVERT: A 1869 MET cc_start: 0.8219 (tpt) cc_final: 0.7946 (tpt) REVERT: A 2315 MET cc_start: 0.7514 (mmm) cc_final: 0.6559 (mmp) REVERT: A 2393 LEU cc_start: 0.6877 (mm) cc_final: 0.5590 (pp) outliers start: 37 outliers final: 29 residues processed: 154 average time/residue: 0.1321 time to fit residues: 35.8974 Evaluate side-chains 156 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1185 PHE Chi-restraints excluded: chain B residue 1288 MET Chi-restraints excluded: chain B residue 1326 LEU Chi-restraints excluded: chain B residue 1470 THR Chi-restraints excluded: chain B residue 1750 VAL Chi-restraints excluded: chain B residue 1752 SER Chi-restraints excluded: chain B residue 1861 LEU Chi-restraints excluded: chain B residue 1935 LEU Chi-restraints excluded: chain B residue 2104 TRP Chi-restraints excluded: chain B residue 2115 LEU Chi-restraints excluded: chain B residue 2137 LEU Chi-restraints excluded: chain B residue 2167 ILE Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1185 PHE Chi-restraints excluded: chain A residue 1485 TYR Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1584 HIS Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 2202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 84 optimal weight: 10.0000 chunk 297 optimal weight: 3.9990 chunk 294 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 263 optimal weight: 0.0020 chunk 262 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 ASN ** 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 = 0.4051 r_free = 0.4051 target = 0.109200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.078731 restraints weight = 75707.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.082168 restraints weight = 43561.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.082678 restraints weight = 27630.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.083325 restraints weight = 22884.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.083646 restraints weight = 21340.126| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24676 Z= 0.134 Angle : 0.581 11.425 33780 Z= 0.290 Chirality : 0.042 0.163 4226 Planarity : 0.003 0.037 4230 Dihedral : 5.913 108.411 3614 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.45 % Allowed : 16.04 % Favored : 82.51 % 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: -0.42 (0.15), residues: 3346 helix: 1.44 (0.17), residues: 1066 sheet: -1.28 (0.21), residues: 636 loop : -0.98 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1866 TYR 0.012 0.001 TYR B1402 PHE 0.015 0.001 PHE A1227 TRP 0.024 0.002 TRP A1376 HIS 0.007 0.001 HIS B1043 Details of bonding type rmsd covalent geometry : bond 0.00311 (24676) covalent geometry : angle 0.58069 (33780) hydrogen bonds : bond 0.03036 ( 966) hydrogen bonds : angle 4.22045 ( 2571) ********************** 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 156 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1185 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.6549 (m-80) REVERT: B 2104 TRP cc_start: 0.9097 (OUTLIER) cc_final: 0.8520 (t60) REVERT: B 2137 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7492 (mp) REVERT: A 712 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8319 (mpp) REVERT: A 1057 MET cc_start: 0.6844 (mtm) cc_final: 0.6558 (mtt) REVERT: A 1099 PRO cc_start: 0.8436 (Cg_exo) cc_final: 0.8223 (Cg_endo) REVERT: A 1175 MET cc_start: 0.6061 (ptp) cc_final: 0.5643 (ptp) REVERT: A 1869 MET cc_start: 0.8229 (tpt) cc_final: 0.7946 (tpt) REVERT: A 2315 MET cc_start: 0.7547 (mmm) cc_final: 0.6596 (mmp) REVERT: A 2393 LEU cc_start: 0.6890 (mm) cc_final: 0.5603 (pp) outliers start: 33 outliers final: 29 residues processed: 148 average time/residue: 0.1383 time to fit residues: 35.9755 Evaluate side-chains 156 residues out of total 3074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1185 PHE Chi-restraints excluded: chain B residue 1288 MET Chi-restraints excluded: chain B residue 1326 LEU Chi-restraints excluded: chain B residue 1470 THR Chi-restraints excluded: chain B residue 1750 VAL Chi-restraints excluded: chain B residue 1752 SER Chi-restraints excluded: chain B residue 1861 LEU Chi-restraints excluded: chain B residue 1935 LEU Chi-restraints excluded: chain B residue 2104 TRP Chi-restraints excluded: chain B residue 2115 LEU Chi-restraints excluded: chain B residue 2137 LEU Chi-restraints excluded: chain B residue 2167 ILE Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1185 PHE Chi-restraints excluded: chain A residue 1485 TYR Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1584 HIS Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 2202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 257 optimal weight: 2.9990 chunk 41 optimal weight: 0.0370 chunk 71 optimal weight: 0.0370 chunk 148 optimal weight: 0.0020 chunk 188 optimal weight: 0.9990 chunk 147 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 142 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.3946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 ASN ** 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 = 0.4051 r_free = 0.4051 target = 0.109206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.078724 restraints weight = 75774.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.082123 restraints weight = 43638.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.082685 restraints weight = 27658.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.083361 restraints weight = 22855.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.083612 restraints weight = 21852.792| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24676 Z= 0.133 Angle : 0.580 11.407 33780 Z= 0.290 Chirality : 0.042 0.162 4226 Planarity : 0.003 0.037 4230 Dihedral : 5.924 108.411 3614 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.45 % Allowed : 16.04 % Favored : 82.51 % 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: -0.42 (0.15), residues: 3346 helix: 1.44 (0.17), residues: 1066 sheet: -1.28 (0.21), residues: 636 loop : -0.98 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1866 TYR 0.012 0.001 TYR B1402 PHE 0.014 0.001 PHE A1227 TRP 0.024 0.002 TRP A1376 HIS 0.007 0.001 HIS B1043 Details of bonding type rmsd covalent geometry : bond 0.00310 (24676) covalent geometry : angle 0.58022 (33780) hydrogen bonds : bond 0.03034 ( 966) hydrogen bonds : angle 4.22013 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4098.93 seconds wall clock time: 71 minutes 29.12 seconds (4289.12 seconds total)