Starting phenix.real_space_refine on Thu Jul 2 23:27:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pw6_13676/07_2026/7pw6_13676.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pw6_13676/07_2026/7pw6_13676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pw6_13676/07_2026/7pw6_13676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pw6_13676/07_2026/7pw6_13676.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7pw6_13676/07_2026/7pw6_13676.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pw6_13676/07_2026/7pw6_13676.cif" model { file = "/net/cci-nas-00/data/ceres_data/7pw6_13676/07_2026/7pw6_13676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pw6_13676/07_2026/7pw6_13676.cif" } resolution = 3.05 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= 0.003 sd= 0.073 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 6 5.49 5 S 53 5.16 5 Cl 1 4.86 5 C 6645 2.51 5 N 1851 2.21 5 O 1837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10393 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5740 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 25, 'TRANS': 741} Chain breaks: 12 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 407 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 30, 'ASP:plan': 19, 'ASN:plan1': 9, 'ARG:plan': 1, 'GLN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 226 Chain: "A" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1439 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain breaks: 6 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'UNK:plan-1': 42, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 6, 'GLN:plan1': 8, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 150 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 196 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'UNK:plan-1': 16, 'GLU:plan': 3, 'TRP:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2943 Classifications: {'peptide': 395} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 18, 'TRANS': 376} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'UNK:plan-1': 16, 'ARG:plan': 3, 'GLU:plan': 16, 'ASN:plan1': 1, 'ASP:plan': 6, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 124 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'88C': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.08, per 1000 atoms: 0.20 Number of scatterers: 10393 At special positions: 0 Unit cell: (120.87, 105.549, 107.251, 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) Cl 1 17.00 S 53 16.00 P 6 15.00 O 1837 8.00 N 1851 7.00 C 6645 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: 2.19 Conformation dependent library (CDL) restraints added in 368.9 milliseconds 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2718 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 3 sheets defined 76.8% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 792 through 806 removed outlier: 3.652A pdb=" N ARG A 797 " --> pdb=" O ASP A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 823 removed outlier: 3.560A pdb=" N LYS A 819 " --> pdb=" O GLN A 815 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 835 through 851 removed outlier: 3.530A pdb=" N ILE A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 872 Processing helix chain 'A' and resid 882 through 891 Processing helix chain 'A' and resid 902 through 907 removed outlier: 4.041A pdb=" N LYS A 907 " --> pdb=" O ASN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 927 Processing helix chain 'A' and resid 935 through 956 removed outlier: 3.638A pdb=" N THR A 939 " --> pdb=" O ARG A 935 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE A 940 " --> pdb=" O ALA A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 999 removed outlier: 3.831A pdb=" N HIS A 973 " --> pdb=" O ASN A 969 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY A 974 " --> pdb=" O ASP A 970 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN A 977 " --> pdb=" O HIS A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1019 removed outlier: 3.567A pdb=" N THR A1018 " --> pdb=" O THR A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1041 removed outlier: 4.446A pdb=" N LEU A1032 " --> pdb=" O THR A1028 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N SER A1033 " --> pdb=" O ARG A1029 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A1036 " --> pdb=" O LEU A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1058 removed outlier: 3.778A pdb=" N THR A1047 " --> pdb=" O GLN A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1084 Processing helix chain 'A' and resid 1085 through 1097 Processing helix chain 'A' and resid 1106 through 1115 removed outlier: 3.550A pdb=" N GLN A1113 " --> pdb=" O SER A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1134 Processing helix chain 'A' and resid 1143 through 1151 removed outlier: 3.677A pdb=" N LEU A1149 " --> pdb=" O SER A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1197 removed outlier: 3.833A pdb=" N ASN A1184 " --> pdb=" O PRO A1180 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A1197 " --> pdb=" O CYS A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1218 Processing helix chain 'A' and resid 1227 through 1239 Processing helix chain 'A' and resid 1242 through 1250 Processing helix chain 'A' and resid 1281 through 1305 removed outlier: 3.511A pdb=" N LEU A1285 " --> pdb=" O ASP A1281 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN A1305 " --> pdb=" O ALA A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1332 removed outlier: 3.615A pdb=" N ILE A1332 " --> pdb=" O SER A1328 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1341 removed outlier: 3.781A pdb=" N THR A1341 " --> pdb=" O LEU A1337 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1367 Processing helix chain 'A' and resid 1370 through 1374 removed outlier: 3.680A pdb=" N LEU A1374 " --> pdb=" O GLU A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1384 removed outlier: 3.619A pdb=" N ARG A1383 " --> pdb=" O GLU A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1407 removed outlier: 3.738A pdb=" N TYR A1399 " --> pdb=" O GLN A1395 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A1402 " --> pdb=" O ARG A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1410 No H-bonds generated for 'chain 'A' and resid 1408 through 1410' Processing helix chain 'A' and resid 1417 through 1434 Processing helix chain 'A' and resid 1437 through 1450 Processing helix chain 'A' and resid 1458 through 1466 removed outlier: 3.766A pdb=" N LEU A1462 " --> pdb=" O THR A1458 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A1463 " --> pdb=" O ALA A1459 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A1464 " --> pdb=" O GLN A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1494 Processing helix chain 'A' and resid 1496 through 1512 Processing helix chain 'A' and resid 1518 through 1535 removed outlier: 4.016A pdb=" N ALA A1522 " --> pdb=" O GLU A1518 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A1523 " --> pdb=" O TYR A1519 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A1528 " --> pdb=" O SER A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1551 removed outlier: 5.052A pdb=" N GLY A1541 " --> pdb=" O LYS A1537 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLN A1542 " --> pdb=" O GLU A1538 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS A1551 " --> pdb=" O TYR A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1559 through 1570 removed outlier: 3.504A pdb=" N THR A1567 " --> pdb=" O LYS A1563 " (cutoff:3.500A) Processing helix chain 'A' and resid 1595 through 1612 removed outlier: 3.571A pdb=" N PHE A1599 " --> pdb=" O GLY A1595 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE A1600 " --> pdb=" O GLU A1596 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A1601 " --> pdb=" O PRO A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1637 removed outlier: 3.823A pdb=" N TRP A1619 " --> pdb=" O VAL A1615 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A1622 " --> pdb=" O SER A1618 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A1632 " --> pdb=" O ARG A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1656 Processing helix chain 'A' and resid 1664 through 1674 Processing helix chain 'A' and resid 1704 through 1717 Processing helix chain 'A' and resid 1728 through 1741 removed outlier: 3.714A pdb=" N VAL A1732 " --> pdb=" O GLY A1728 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1757 Processing helix chain 'A' and resid 1781 through 1799 removed outlier: 3.813A pdb=" N ALA A1788 " --> pdb=" O MET A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1812 removed outlier: 3.909A pdb=" N HIS A1809 " --> pdb=" O GLN A1805 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A1812 " --> pdb=" O GLU A1808 " (cutoff:3.500A) Processing helix chain 'A' and resid 1816 through 1820 removed outlier: 3.727A pdb=" N ARG A1820 " --> pdb=" O ALA A1817 " (cutoff:3.500A) Processing helix chain 'A' and resid 1822 through 1829 Processing helix chain 'A' and resid 1834 through 1850 removed outlier: 3.834A pdb=" N ARG A1838 " --> pdb=" O GLU A1834 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A1850 " --> pdb=" O CYS A1846 " (cutoff:3.500A) Processing helix chain 'A' and resid 1856 through 1865 removed outlier: 3.618A pdb=" N ALA A1860 " --> pdb=" O ILE A1856 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A1865 " --> pdb=" O ILE A1861 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1939 removed outlier: 4.382A pdb=" N CYS A1929 " --> pdb=" O MET A1925 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TYR A1930 " --> pdb=" O MET A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1958 Processing helix chain 'A' and resid 1963 through 1976 Processing helix chain 'A' and resid 2007 through 2020 Processing helix chain 'A' and resid 2036 through 2045 Processing helix chain 'A' and resid 2046 through 2056 removed outlier: 3.973A pdb=" N LYS A2056 " --> pdb=" O LEU A2052 " (cutoff:3.500A) Processing helix chain 'A' and resid 2069 through 2083 removed outlier: 3.689A pdb=" N UNK A2083 " --> pdb=" O UNK A2079 " (cutoff:3.500A) Processing helix chain 'A' and resid 2160 through 2176 removed outlier: 3.668A pdb=" N GLU A2164 " --> pdb=" O LEU A2160 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A2165 " --> pdb=" O HIS A2161 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A2176 " --> pdb=" O ILE A2172 " (cutoff:3.500A) Processing helix chain 'A' and resid 2177 through 2178 No H-bonds generated for 'chain 'A' and resid 2177 through 2178' Processing helix chain 'A' and resid 2179 through 2183 removed outlier: 3.672A pdb=" N GLN A2183 " --> pdb=" O ILE A2180 " (cutoff:3.500A) Processing helix chain 'A' and resid 2214 through 2232 removed outlier: 3.760A pdb=" N TYR A2218 " --> pdb=" O LEU A2214 " (cutoff:3.500A) Processing helix chain 'A' and resid 2250 through 2265 removed outlier: 3.584A pdb=" N LYS A2256 " --> pdb=" O LEU A2252 " (cutoff:3.500A) Proline residue: A2259 - end of helix removed outlier: 3.661A pdb=" N VAL A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A2265 " --> pdb=" O LEU A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2276 through 2289 removed outlier: 3.555A pdb=" N MET A2280 " --> pdb=" O PRO A2276 " (cutoff:3.500A) Processing helix chain 'A' and resid 2294 through 2304 Processing helix chain 'A' and resid 2306 through 2332 Processing helix chain 'A' and resid 2337 through 2339 No H-bonds generated for 'chain 'A' and resid 2337 through 2339' Processing helix chain 'A' and resid 2361 through 2365 Processing helix chain 'A' and resid 2376 through 2382 Processing helix chain 'A' and resid 2390 through 2406 Processing helix chain 'A' and resid 2406 through 2419 removed outlier: 3.813A pdb=" N LEU A2410 " --> pdb=" O GLY A2406 " (cutoff:3.500A) Processing helix chain 'A' and resid 3608 through 3622 Processing helix chain 'A' and resid 3632 through 3646 Processing helix chain 'A' and resid 3646 through 3652 removed outlier: 3.694A pdb=" N LEU A3650 " --> pdb=" O ASN A3646 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A3652 " --> pdb=" O ASP A3648 " (cutoff:3.500A) Processing helix chain 'A' and resid 3654 through 3658 Processing sheet with id=AA1, first strand: chain 'A' and resid 2089 through 2091 removed outlier: 3.576A pdb=" N ILE A2128 " --> pdb=" O LEU A2090 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N THR A2127 " --> pdb=" O LEU A2141 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU A2141 " --> pdb=" O THR A2127 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU A2141 " --> pdb=" O VAL A2124 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N VAL A2124 " --> pdb=" O LEU A2141 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A2143 " --> pdb=" O HIS A2122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2089 through 2091 removed outlier: 3.576A pdb=" N ILE A2128 " --> pdb=" O LEU A2090 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N THR A2127 " --> pdb=" O LEU A2141 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU A2141 " --> pdb=" O THR A2127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2211 through 2213 696 hydrogen bonds defined for protein. 2043 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: 1.88 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3009 1.34 - 1.45: 1536 1.45 - 1.57: 5952 1.57 - 1.69: 7 1.69 - 1.81: 80 Bond restraints: 10584 Sorted by residual: bond pdb=" C13 88C A3702 " pdb=" N35 88C A3702 " ideal model delta sigma weight residual 1.325 1.398 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C28 88C A3702 " pdb=" N30 88C A3702 " ideal model delta sigma weight residual 1.352 1.424 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C26 88C A3702 " pdb=" N27 88C A3702 " ideal model delta sigma weight residual 1.391 1.462 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C28 88C A3702 " pdb=" N27 88C A3702 " ideal model delta sigma weight residual 1.376 1.443 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C13 88C A3702 " pdb=" N12 88C A3702 " ideal model delta sigma weight residual 1.364 1.417 -0.053 2.00e-02 2.50e+03 7.14e+00 ... (remaining 10579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 14160 1.82 - 3.64: 213 3.64 - 5.46: 54 5.46 - 7.27: 10 7.27 - 9.09: 10 Bond angle restraints: 14447 Sorted by residual: angle pdb=" C ALA A1002 " pdb=" N ASN A1003 " pdb=" CA ASN A1003 " ideal model delta sigma weight residual 121.54 128.41 -6.87 1.91e+00 2.74e-01 1.29e+01 angle pdb=" N VAL A1390 " pdb=" CA VAL A1390 " pdb=" C VAL A1390 " ideal model delta sigma weight residual 112.83 109.30 3.53 9.90e-01 1.02e+00 1.27e+01 angle pdb=" O12 IHP A3701 " pdb=" P2 IHP A3701 " pdb=" O32 IHP A3701 " ideal model delta sigma weight residual 100.47 109.56 -9.09 3.00e+00 1.11e-01 9.19e+00 angle pdb=" C09 88C A3702 " pdb=" S06 88C A3702 " pdb=" N03 88C A3702 " ideal model delta sigma weight residual 102.09 110.79 -8.70 3.00e+00 1.11e-01 8.42e+00 angle pdb=" O16 IHP A3701 " pdb=" P6 IHP A3701 " pdb=" O36 IHP A3701 " ideal model delta sigma weight residual 101.25 109.51 -8.26 3.00e+00 1.11e-01 7.58e+00 ... (remaining 14442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 5695 16.63 - 33.26: 458 33.26 - 49.89: 87 49.89 - 66.52: 22 66.52 - 83.15: 15 Dihedral angle restraints: 6277 sinusoidal: 2131 harmonic: 4146 Sorted by residual: dihedral pdb=" CA ASP A1136 " pdb=" CB ASP A1136 " pdb=" CG ASP A1136 " pdb=" OD1 ASP A1136 " ideal model delta sinusoidal sigma weight residual -30.00 -89.18 59.18 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CG ARG A1398 " pdb=" CD ARG A1398 " pdb=" NE ARG A1398 " pdb=" CZ ARG A1398 " ideal model delta sinusoidal sigma weight residual 90.00 133.10 -43.10 2 1.50e+01 4.44e-03 9.96e+00 dihedral pdb=" CG ARG A1029 " pdb=" CD ARG A1029 " pdb=" NE ARG A1029 " pdb=" CZ ARG A1029 " ideal model delta sinusoidal sigma weight residual 180.00 138.16 41.84 2 1.50e+01 4.44e-03 9.49e+00 ... (remaining 6274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.005: 1751 1.005 - 2.010: 0 2.010 - 3.015: 0 3.015 - 4.020: 0 4.020 - 5.026: 3 Chirality restraints: 1754 Sorted by residual: chirality pdb=" C2 IHP A3701 " pdb=" C1 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O12 IHP A3701 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.31e+02 chirality pdb=" C4 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" C5 IHP A3701 " pdb=" O14 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.48 -2.52 5.00 2.00e-01 2.50e+01 6.26e+02 chirality pdb=" C1 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C6 IHP A3701 " pdb=" O11 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.32 -2.48 4.80 2.00e-01 2.50e+01 5.75e+02 ... (remaining 1751 not shown) Planarity restraints: 1790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A2246 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.95e+00 pdb=" N PRO A2247 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A2247 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A2247 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A1333 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO A1334 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A1334 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1334 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1281 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO A1282 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A1282 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1282 " -0.023 5.00e-02 4.00e+02 ... (remaining 1787 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 134 2.70 - 3.25: 10175 3.25 - 3.80: 16100 3.80 - 4.35: 19688 4.35 - 4.90: 34247 Nonbonded interactions: 80344 Sorted by model distance: nonbonded pdb=" OH TYR A2193 " pdb=" O ILE A2353 " model vdw 2.146 3.040 nonbonded pdb=" O TRP A1106 " pdb=" OG SER A1109 " model vdw 2.172 3.040 nonbonded pdb=" O GLU A1068 " pdb=" OG1 THR A1072 " model vdw 2.285 3.040 nonbonded pdb=" O GLN A 963 " pdb=" NH2 ARG A 979 " model vdw 2.285 3.120 nonbonded pdb=" OE1 GLU A 991 " pdb=" NH2 ARG A1049 " model vdw 2.298 3.120 ... (remaining 80339 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.520 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: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 10.700 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 : 0.003 0.073 10584 Z= 0.169 Angle : 0.647 9.093 14447 Z= 0.346 Chirality : 0.208 5.026 1754 Planarity : 0.004 0.075 1790 Dihedral : 13.504 83.154 3559 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.10 % Allowed : 0.10 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.97 (0.24), residues: 1298 helix: 2.42 (0.18), residues: 878 sheet: -0.27 (0.80), residues: 36 loop : -1.28 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 930 TYR 0.020 0.001 TYR A 998 PHE 0.012 0.001 PHE A1827 TRP 0.016 0.001 TRP A1393 HIS 0.007 0.001 HIS A2352 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (10584) covalent geometry : angle 0.64687 / 0.35 (14447) hydrogen bonds : bond 0.13375 / 9.04 ( 693) hydrogen bonds : angle 4.46328 / 3.47 ( 2043) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.388 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.1165 time to fit residues: 18.3623 Evaluate side-chains 81 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.0980 chunk 55 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1344 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.142215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.125436 restraints weight = 14204.896| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.33 r_work: 0.3309 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10584 Z= 0.113 Angle : 0.500 10.657 14447 Z= 0.238 Chirality : 0.039 0.490 1754 Planarity : 0.004 0.059 1790 Dihedral : 2.962 38.303 1520 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.52 % Allowed : 6.95 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.30 (0.24), residues: 1298 helix: 2.59 (0.18), residues: 886 sheet: 0.24 (0.88), residues: 38 loop : -1.07 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1329 TYR 0.023 0.001 TYR A 998 PHE 0.010 0.001 PHE A1016 TRP 0.008 0.001 TRP A2221 HIS 0.004 0.001 HIS A2337 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (10584) covalent geometry : angle 0.49963 / 0.24 (14447) hydrogen bonds : bond 0.03992 / 2.74 ( 693) hydrogen bonds : angle 3.39930 / 2.63 ( 2043) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.284 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 88 average time/residue: 0.1047 time to fit residues: 13.1134 Evaluate side-chains 82 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1130 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 127 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.0060 chunk 105 optimal weight: 2.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.139876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.123016 restraints weight = 14210.343| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.31 r_work: 0.3279 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10584 Z= 0.119 Angle : 0.469 8.725 14447 Z= 0.231 Chirality : 0.038 0.392 1754 Planarity : 0.004 0.053 1790 Dihedral : 3.365 42.192 1520 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.45 % Allowed : 7.57 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.29 (0.24), residues: 1298 helix: 2.60 (0.18), residues: 881 sheet: 0.33 (0.86), residues: 38 loop : -1.07 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1329 TYR 0.022 0.001 TYR A 998 PHE 0.012 0.001 PHE A 940 TRP 0.009 0.001 TRP A2207 HIS 0.004 0.001 HIS A2337 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (10584) covalent geometry : angle 0.46888 / 0.23 (14447) hydrogen bonds : bond 0.04142 / 2.85 ( 693) hydrogen bonds : angle 3.29656 / 2.54 ( 2043) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.298 Fit side-chains REVERT: A 2196 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.8995 (p) outliers start: 14 outliers final: 10 residues processed: 95 average time/residue: 0.0961 time to fit residues: 13.2565 Evaluate side-chains 88 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1533 GLN Chi-restraints excluded: chain A residue 1744 TYR Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2288 MET Chi-restraints excluded: chain A residue 2409 THR Chi-restraints excluded: chain A residue 3661 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 121 optimal weight: 3.9990 chunk 41 optimal weight: 0.0050 chunk 116 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.120282 restraints weight = 14339.571| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.30 r_work: 0.3264 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10584 Z= 0.123 Angle : 0.472 8.363 14447 Z= 0.232 Chirality : 0.038 0.383 1754 Planarity : 0.004 0.050 1790 Dihedral : 3.438 44.319 1520 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.35 % Allowed : 7.88 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.28 (0.24), residues: 1298 helix: 2.56 (0.18), residues: 881 sheet: 0.33 (0.83), residues: 38 loop : -1.00 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2336 TYR 0.021 0.001 TYR A 998 PHE 0.011 0.001 PHE A1016 TRP 0.009 0.001 TRP A2207 HIS 0.004 0.001 HIS A2337 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (10584) covalent geometry : angle 0.47237 / 0.23 (14447) hydrogen bonds : bond 0.04165 / 2.87 ( 693) hydrogen bonds : angle 3.27960 / 2.53 ( 2043) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.262 Fit side-chains REVERT: A 2196 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.9006 (p) outliers start: 13 outliers final: 11 residues processed: 87 average time/residue: 0.0991 time to fit residues: 12.4273 Evaluate side-chains 87 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1744 TYR Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2288 MET Chi-restraints excluded: chain A residue 2409 THR Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3661 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 36 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120899 restraints weight = 14290.783| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.28 r_work: 0.3255 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10584 Z= 0.138 Angle : 0.484 7.725 14447 Z= 0.240 Chirality : 0.039 0.389 1754 Planarity : 0.004 0.049 1790 Dihedral : 3.545 46.299 1520 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.56 % Allowed : 8.51 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.21 (0.24), residues: 1298 helix: 2.48 (0.17), residues: 882 sheet: 0.36 (0.81), residues: 38 loop : -0.97 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2336 TYR 0.021 0.001 TYR A 998 PHE 0.012 0.001 PHE A1016 TRP 0.010 0.001 TRP A2207 HIS 0.005 0.001 HIS A2337 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (10584) covalent geometry : angle 0.48447 / 0.24 (14447) hydrogen bonds : bond 0.04484 / 3.08 ( 693) hydrogen bonds : angle 3.32720 / 2.57 ( 2043) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.426 Fit side-chains REVERT: A 1784 MET cc_start: 0.8215 (ttt) cc_final: 0.7987 (ttt) REVERT: A 2196 THR cc_start: 0.9289 (OUTLIER) cc_final: 0.9027 (p) outliers start: 15 outliers final: 10 residues processed: 93 average time/residue: 0.1046 time to fit residues: 14.2731 Evaluate side-chains 87 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1744 TYR Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2409 THR Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3661 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 2 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 41 optimal weight: 0.0370 chunk 87 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 81 optimal weight: 0.5980 chunk 74 optimal weight: 0.0980 chunk 53 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.124167 restraints weight = 14332.009| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.10 r_work: 0.3305 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10584 Z= 0.091 Angle : 0.421 7.208 14447 Z= 0.210 Chirality : 0.037 0.378 1754 Planarity : 0.004 0.046 1790 Dihedral : 3.381 49.305 1520 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.45 % Allowed : 9.34 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.55 (0.24), residues: 1298 helix: 2.73 (0.17), residues: 889 sheet: 0.40 (0.83), residues: 38 loop : -0.87 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1329 TYR 0.020 0.001 TYR A 998 PHE 0.009 0.001 PHE A1016 TRP 0.009 0.001 TRP A2221 HIS 0.003 0.001 HIS A2352 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (10584) covalent geometry : angle 0.42060 / 0.21 (14447) hydrogen bonds : bond 0.03234 / 2.24 ( 693) hydrogen bonds : angle 3.11689 / 2.41 ( 2043) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.394 Fit side-chains REVERT: A 2196 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.9012 (p) outliers start: 14 outliers final: 10 residues processed: 96 average time/residue: 0.0992 time to fit residues: 13.9866 Evaluate side-chains 88 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1744 TYR Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2228 LEU Chi-restraints excluded: chain A residue 2288 MET Chi-restraints excluded: chain A residue 2409 THR Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3661 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 130 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.138305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.120372 restraints weight = 14194.695| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.31 r_work: 0.3247 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10584 Z= 0.127 Angle : 0.465 7.232 14447 Z= 0.232 Chirality : 0.038 0.385 1754 Planarity : 0.004 0.046 1790 Dihedral : 3.557 50.809 1520 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.66 % Allowed : 9.85 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.41 (0.24), residues: 1298 helix: 2.60 (0.17), residues: 889 sheet: 0.46 (0.84), residues: 38 loop : -0.88 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2248 TYR 0.021 0.001 TYR A 998 PHE 0.011 0.001 PHE A 817 TRP 0.009 0.001 TRP A2207 HIS 0.004 0.001 HIS A2337 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10584) covalent geometry : angle 0.46470 / 0.23 (14447) hydrogen bonds : bond 0.04196 / 2.89 ( 693) hydrogen bonds : angle 3.23680 / 2.50 ( 2043) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.435 Fit side-chains REVERT: A 1784 MET cc_start: 0.8251 (ttt) cc_final: 0.8025 (ttt) REVERT: A 2196 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.9032 (p) outliers start: 16 outliers final: 12 residues processed: 95 average time/residue: 0.1003 time to fit residues: 14.0658 Evaluate side-chains 91 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1463 VAL Chi-restraints excluded: chain A residue 1744 TYR Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2228 LEU Chi-restraints excluded: chain A residue 2288 MET Chi-restraints excluded: chain A residue 2409 THR Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3661 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 105 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.138361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120571 restraints weight = 14249.355| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.23 r_work: 0.3264 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10584 Z= 0.122 Angle : 0.459 10.029 14447 Z= 0.229 Chirality : 0.038 0.376 1754 Planarity : 0.004 0.045 1790 Dihedral : 3.597 51.653 1520 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.76 % Allowed : 9.96 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.39 (0.24), residues: 1298 helix: 2.57 (0.17), residues: 891 sheet: 0.72 (0.87), residues: 38 loop : -0.89 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 930 TYR 0.020 0.001 TYR A 998 PHE 0.011 0.001 PHE A1016 TRP 0.009 0.001 TRP A2207 HIS 0.004 0.001 HIS A2337 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (10584) covalent geometry : angle 0.45909 / 0.23 (14447) hydrogen bonds : bond 0.04079 / 2.81 ( 693) hydrogen bonds : angle 3.23594 / 2.50 ( 2043) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.414 Fit side-chains REVERT: A 1364 VAL cc_start: 0.8844 (t) cc_final: 0.8637 (t) REVERT: A 1784 MET cc_start: 0.8201 (ttt) cc_final: 0.7966 (ttt) REVERT: A 2153 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8295 (tp) REVERT: A 2196 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.9050 (p) outliers start: 17 outliers final: 15 residues processed: 94 average time/residue: 0.0980 time to fit residues: 13.7063 Evaluate side-chains 95 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1463 VAL Chi-restraints excluded: chain A residue 1744 TYR Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 2153 LEU Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2228 LEU Chi-restraints excluded: chain A residue 2288 MET Chi-restraints excluded: chain A residue 2409 THR Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3657 TRP Chi-restraints excluded: chain A residue 3661 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 6 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 131 optimal weight: 0.4980 chunk 130 optimal weight: 0.0050 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.139244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120475 restraints weight = 14136.953| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.41 r_work: 0.3266 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10584 Z= 0.109 Angle : 0.440 9.947 14447 Z= 0.220 Chirality : 0.037 0.366 1754 Planarity : 0.004 0.045 1790 Dihedral : 3.540 51.773 1520 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.76 % Allowed : 10.06 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.48 (0.24), residues: 1298 helix: 2.65 (0.17), residues: 891 sheet: 0.70 (0.86), residues: 38 loop : -0.86 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2248 TYR 0.021 0.001 TYR A 998 PHE 0.010 0.001 PHE A 817 TRP 0.009 0.001 TRP A2221 HIS 0.004 0.001 HIS A2337 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (10584) covalent geometry : angle 0.43988 / 0.22 (14447) hydrogen bonds : bond 0.03804 / 2.62 ( 693) hydrogen bonds : angle 3.18272 / 2.46 ( 2043) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.299 Fit side-chains REVERT: A 1364 VAL cc_start: 0.8854 (t) cc_final: 0.8611 (t) REVERT: A 2196 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.9033 (p) outliers start: 17 outliers final: 13 residues processed: 94 average time/residue: 0.0962 time to fit residues: 13.3897 Evaluate side-chains 92 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1463 VAL Chi-restraints excluded: chain A residue 1744 TYR Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2228 LEU Chi-restraints excluded: chain A residue 2288 MET Chi-restraints excluded: chain A residue 2409 THR Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3657 TRP Chi-restraints excluded: chain A residue 3661 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 0.0070 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.137587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.118598 restraints weight = 14173.249| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.30 r_work: 0.3246 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10584 Z= 0.140 Angle : 0.485 9.933 14447 Z= 0.242 Chirality : 0.039 0.372 1754 Planarity : 0.004 0.045 1790 Dihedral : 3.666 50.812 1520 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.45 % Allowed : 10.27 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.32 (0.24), residues: 1298 helix: 2.51 (0.17), residues: 890 sheet: 0.78 (0.87), residues: 38 loop : -0.89 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 930 TYR 0.021 0.001 TYR A 998 PHE 0.012 0.001 PHE A 817 TRP 0.009 0.001 TRP A2207 HIS 0.005 0.001 HIS A2337 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (10584) covalent geometry : angle 0.48541 / 0.24 (14447) hydrogen bonds : bond 0.04513 / 3.10 ( 693) hydrogen bonds : angle 3.31130 / 2.56 ( 2043) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.355 Fit side-chains REVERT: A 1364 VAL cc_start: 0.8956 (t) cc_final: 0.8732 (t) REVERT: A 2196 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.9049 (p) outliers start: 14 outliers final: 12 residues processed: 90 average time/residue: 0.0990 time to fit residues: 13.0193 Evaluate side-chains 91 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1463 VAL Chi-restraints excluded: chain A residue 1744 TYR Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2288 MET Chi-restraints excluded: chain A residue 2409 THR Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3657 TRP Chi-restraints excluded: chain A residue 3661 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 134 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 77 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.137474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.118249 restraints weight = 14256.949| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.30 r_work: 0.3243 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10584 Z= 0.144 Angle : 0.486 10.006 14447 Z= 0.242 Chirality : 0.039 0.372 1754 Planarity : 0.004 0.047 1790 Dihedral : 3.716 50.484 1520 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.35 % Allowed : 10.58 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.23 (0.24), residues: 1298 helix: 2.44 (0.17), residues: 891 sheet: 0.80 (0.88), residues: 38 loop : -0.92 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2248 TYR 0.021 0.001 TYR A 998 PHE 0.012 0.001 PHE A 817 TRP 0.010 0.001 TRP A2207 HIS 0.005 0.001 HIS A2337 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (10584) covalent geometry : angle 0.48589 / 0.24 (14447) hydrogen bonds : bond 0.04568 / 3.14 ( 693) hydrogen bonds : angle 3.33967 / 2.58 ( 2043) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2665.64 seconds wall clock time: 46 minutes 23.97 seconds (2783.97 seconds total)