Starting phenix.real_space_refine on Wed Mar 4 04:34:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pw6_13676/03_2026/7pw6_13676.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pw6_13676/03_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_13676/03_2026/7pw6_13676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pw6_13676/03_2026/7pw6_13676.map" model { file = "/net/cci-nas-00/data/ceres_data/7pw6_13676/03_2026/7pw6_13676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pw6_13676/03_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-5986/lib/python3.9/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: 2.10, 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: 0.76 Conformation dependent library (CDL) restraints added in 476.2 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: 0.35 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: 1.84 Time building geometry restraints manager: 0.96 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 - 33.03: 6175 33.03 - 66.06: 116 66.06 - 99.09: 23 99.09 - 132.12: 4 132.12 - 165.16: 3 Dihedral angle restraints: 6321 sinusoidal: 2175 harmonic: 4146 Sorted by residual: dihedral pdb=" C6 IHP A3701 " pdb=" C1 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" O12 IHP A3701 " ideal model delta sinusoidal sigma weight residual 61.05 -104.11 165.16 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C4 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O12 IHP A3701 " ideal model delta sinusoidal sigma weight residual 60.90 -159.10 -140.00 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" O12 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O13 IHP A3701 " ideal model delta sinusoidal sigma weight residual 64.08 -72.56 136.64 1 3.00e+01 1.11e-03 1.84e+01 ... (remaining 6318 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: 5.020 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.010 Find NCS groups from input model: 0.050 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: 0.000 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: 16.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 15.204 165.156 3603 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 covalent geometry : bond 0.00333 (10584) covalent geometry : angle 0.64687 (14447) hydrogen bonds : bond 0.13375 ( 693) hydrogen bonds : angle 4.46328 ( 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 : 0.358 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.1204 time to fit residues: 18.6606 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 : 0.296 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A1344 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.142075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.125172 restraints weight = 14194.092| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.25 r_work: 0.3316 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10584 Z= 0.114 Angle : 0.516 11.623 14447 Z= 0.243 Chirality : 0.037 0.233 1754 Planarity : 0.004 0.059 1790 Dihedral : 8.665 99.590 1564 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.73 % Allowed : 6.64 % Favored : 92.63 % 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: 2.27 (0.24), residues: 1298 helix: 2.57 (0.18), residues: 887 sheet: 0.23 (0.88), residues: 38 loop : -1.10 (0.32), residues: 373 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 A2352 Details of bonding type rmsd covalent geometry : bond 0.00262 (10584) covalent geometry : angle 0.51644 (14447) hydrogen bonds : bond 0.03871 ( 693) hydrogen bonds : angle 3.37769 ( 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 92 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.323 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 91 average time/residue: 0.1078 time to fit residues: 13.8829 Evaluate side-chains 84 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 3661 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 127 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 105 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.137410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.120458 restraints weight = 14304.805| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.27 r_work: 0.3263 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10584 Z= 0.160 Angle : 0.538 10.692 14447 Z= 0.263 Chirality : 0.039 0.194 1754 Planarity : 0.005 0.055 1790 Dihedral : 7.834 93.114 1564 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.45 % Allowed : 7.99 % Favored : 90.56 % 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: 2.01 (0.24), residues: 1298 helix: 2.37 (0.18), residues: 878 sheet: 0.34 (0.84), residues: 38 loop : -1.10 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1329 TYR 0.022 0.001 TYR A 998 PHE 0.016 0.002 PHE A 940 TRP 0.012 0.001 TRP A2207 HIS 0.005 0.001 HIS A2337 Details of bonding type rmsd covalent geometry : bond 0.00383 (10584) covalent geometry : angle 0.53757 (14447) hydrogen bonds : bond 0.05072 ( 693) hydrogen bonds : angle 3.48801 ( 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 : 0.349 Fit side-chains REVERT: A 1784 MET cc_start: 0.8185 (ttt) cc_final: 0.7786 (ttt) REVERT: A 2196 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.9019 (p) outliers start: 14 outliers final: 8 residues processed: 94 average time/residue: 0.1006 time to fit residues: 13.6089 Evaluate side-chains 83 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 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: 0.0670 chunk 116 optimal weight: 0.9990 chunk 83 optimal weight: 0.0070 chunk 56 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.138831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.122361 restraints weight = 14371.100| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.12 r_work: 0.3281 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1570 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= 0.108 Angle : 0.466 8.862 14447 Z= 0.227 Chirality : 0.036 0.157 1754 Planarity : 0.004 0.050 1790 Dihedral : 7.891 89.682 1564 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.66 % Allowed : 8.82 % Favored : 89.52 % 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: 2.27 (0.24), residues: 1298 helix: 2.52 (0.17), residues: 889 sheet: 0.28 (0.83), residues: 38 loop : -0.99 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1794 TYR 0.020 0.001 TYR A 998 PHE 0.010 0.001 PHE A1016 TRP 0.009 0.001 TRP A2207 HIS 0.004 0.001 HIS A2337 Details of bonding type rmsd covalent geometry : bond 0.00247 (10584) covalent geometry : angle 0.46551 (14447) hydrogen bonds : bond 0.03819 ( 693) hydrogen bonds : angle 3.25768 ( 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 96 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.444 Fit side-chains REVERT: A 1364 VAL cc_start: 0.8788 (t) cc_final: 0.8559 (t) REVERT: A 2196 THR cc_start: 0.9257 (OUTLIER) cc_final: 0.9006 (p) outliers start: 16 outliers final: 10 residues processed: 93 average time/residue: 0.1106 time to fit residues: 14.7492 Evaluate side-chains 89 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.137787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121078 restraints weight = 14297.682| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.27 r_work: 0.3258 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10584 Z= 0.132 Angle : 0.478 7.574 14447 Z= 0.237 Chirality : 0.037 0.170 1754 Planarity : 0.004 0.049 1790 Dihedral : 8.229 90.437 1564 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.66 % Allowed : 9.34 % Favored : 89.00 % 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: 888 sheet: 0.22 (0.82), residues: 38 loop : -0.98 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 930 TYR 0.021 0.001 TYR A 998 PHE 0.011 0.001 PHE A1016 TRP 0.010 0.001 TRP A2207 HIS 0.005 0.001 HIS A2337 Details of bonding type rmsd covalent geometry : bond 0.00313 (10584) covalent geometry : angle 0.47763 (14447) hydrogen bonds : bond 0.04402 ( 693) hydrogen bonds : angle 3.31653 ( 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 94 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.388 Fit side-chains REVERT: A 1364 VAL cc_start: 0.8918 (t) cc_final: 0.8685 (t) REVERT: A 1784 MET cc_start: 0.8217 (ttt) cc_final: 0.7996 (ttt) REVERT: A 2136 LYS cc_start: 0.8682 (mmpt) cc_final: 0.8467 (mmtp) REVERT: A 2196 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.9026 (p) outliers start: 16 outliers final: 13 residues processed: 91 average time/residue: 0.1014 time to fit residues: 13.2344 Evaluate side-chains 88 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 2 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 41 optimal weight: 0.3980 chunk 87 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 chunk 74 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119186 restraints weight = 14334.116| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.44 r_work: 0.3255 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10584 Z= 0.117 Angle : 0.451 7.397 14447 Z= 0.226 Chirality : 0.037 0.186 1754 Planarity : 0.004 0.047 1790 Dihedral : 7.990 91.334 1564 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.76 % Allowed : 9.75 % 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: 2.30 (0.24), residues: 1298 helix: 2.54 (0.17), residues: 889 sheet: 0.27 (0.83), residues: 38 loop : -0.95 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 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 covalent geometry : bond 0.00273 (10584) covalent geometry : angle 0.45104 (14447) hydrogen bonds : bond 0.04031 ( 693) hydrogen bonds : angle 3.24499 ( 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 99 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.342 Fit side-chains REVERT: A 959 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6945 (tt0) REVERT: A 1364 VAL cc_start: 0.8875 (t) cc_final: 0.8622 (t) REVERT: A 2196 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.9038 (p) outliers start: 17 outliers final: 13 residues processed: 96 average time/residue: 0.0972 time to fit residues: 13.8143 Evaluate side-chains 90 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 959 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 130 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.138395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122286 restraints weight = 14195.279| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.21 r_work: 0.3260 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10584 Z= 0.118 Angle : 0.455 7.614 14447 Z= 0.228 Chirality : 0.037 0.192 1754 Planarity : 0.004 0.046 1790 Dihedral : 7.829 90.048 1564 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.97 % Allowed : 9.85 % 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: 2.32 (0.24), residues: 1298 helix: 2.55 (0.17), residues: 890 sheet: 0.40 (0.85), residues: 38 loop : -0.96 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 930 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 covalent geometry : bond 0.00276 (10584) covalent geometry : angle 0.45501 (14447) hydrogen bonds : bond 0.04052 ( 693) hydrogen bonds : angle 3.24403 ( 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 99 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.360 Fit side-chains REVERT: A 959 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6913 (tt0) REVERT: A 1364 VAL cc_start: 0.8884 (t) cc_final: 0.8632 (t) REVERT: A 1784 MET cc_start: 0.8217 (ttt) cc_final: 0.7972 (ttt) REVERT: A 2153 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8267 (tp) REVERT: A 2196 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.9028 (p) outliers start: 19 outliers final: 15 residues processed: 96 average time/residue: 0.1019 time to fit residues: 14.3936 Evaluate side-chains 96 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 959 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 105 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.136836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119642 restraints weight = 14244.913| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.29 r_work: 0.3242 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1882 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= 0.143 Angle : 0.488 7.708 14447 Z= 0.244 Chirality : 0.038 0.200 1754 Planarity : 0.004 0.046 1790 Dihedral : 7.867 89.565 1564 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.07 % Allowed : 9.96 % Favored : 87.97 % 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: 2.20 (0.24), residues: 1298 helix: 2.45 (0.17), residues: 889 sheet: 0.43 (0.85), residues: 38 loop : -0.98 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 930 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 covalent geometry : bond 0.00343 (10584) covalent geometry : angle 0.48771 (14447) hydrogen bonds : bond 0.04596 ( 693) hydrogen bonds : angle 3.33962 ( 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 99 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.382 Fit side-chains REVERT: A 1784 MET cc_start: 0.8250 (ttt) cc_final: 0.8047 (ttt) REVERT: A 2196 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.9036 (p) outliers start: 20 outliers final: 17 residues processed: 96 average time/residue: 0.1029 time to fit residues: 14.5148 Evaluate side-chains 96 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 959 GLN 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 1589 THR Chi-restraints excluded: chain A residue 1744 TYR 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: 2.9990 chunk 67 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 133 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.138042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119099 restraints weight = 14116.875| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.29 r_work: 0.3249 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10584 Z= 0.130 Angle : 0.471 10.048 14447 Z= 0.235 Chirality : 0.037 0.200 1754 Planarity : 0.004 0.046 1790 Dihedral : 7.800 88.966 1564 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.87 % Allowed : 10.27 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.24 (0.24), residues: 1298 helix: 2.49 (0.17), residues: 889 sheet: 0.47 (0.86), residues: 38 loop : -0.98 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1794 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 covalent geometry : bond 0.00308 (10584) covalent geometry : angle 0.47124 (14447) hydrogen bonds : bond 0.04307 ( 693) hydrogen bonds : angle 3.30010 ( 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 98 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.413 Fit side-chains REVERT: A 2153 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8259 (tp) REVERT: A 2196 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.9051 (p) outliers start: 18 outliers final: 16 residues processed: 95 average time/residue: 0.1098 time to fit residues: 14.8766 Evaluate side-chains 96 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 959 GLN 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 1589 THR Chi-restraints excluded: chain A residue 1744 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 56 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 47 optimal weight: 0.0050 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 44 optimal weight: 0.0010 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 922 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120725 restraints weight = 14153.566| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.30 r_work: 0.3279 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10584 Z= 0.104 Angle : 0.445 10.042 14447 Z= 0.222 Chirality : 0.036 0.196 1754 Planarity : 0.004 0.046 1790 Dihedral : 7.600 87.571 1564 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.97 % Allowed : 10.37 % Favored : 87.66 % 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: 2.43 (0.24), residues: 1298 helix: 2.62 (0.17), residues: 891 sheet: 0.50 (0.86), residues: 38 loop : -0.90 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1794 TYR 0.020 0.001 TYR A 998 PHE 0.009 0.001 PHE A 817 TRP 0.009 0.001 TRP A2221 HIS 0.004 0.001 HIS A2352 Details of bonding type rmsd covalent geometry : bond 0.00237 (10584) covalent geometry : angle 0.44528 (14447) hydrogen bonds : bond 0.03625 ( 693) hydrogen bonds : angle 3.19015 ( 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 103 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.433 Fit side-chains REVERT: A 959 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6923 (tt0) REVERT: A 2196 THR cc_start: 0.9242 (OUTLIER) cc_final: 0.9013 (p) outliers start: 19 outliers final: 14 residues processed: 100 average time/residue: 0.1032 time to fit residues: 15.0594 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 : 0.391 ------------------------------------------------------------------------------- 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 959 GLN 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 1589 THR 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 134 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 77 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.138673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.119339 restraints weight = 14220.821| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.39 r_work: 0.3252 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10584 Z= 0.120 Angle : 0.461 10.018 14447 Z= 0.230 Chirality : 0.037 0.195 1754 Planarity : 0.004 0.045 1790 Dihedral : 7.581 87.006 1564 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.66 % Allowed : 10.37 % Favored : 87.97 % 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: 2.38 (0.24), residues: 1298 helix: 2.56 (0.17), residues: 892 sheet: 0.79 (0.89), residues: 38 loop : -0.91 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1794 TYR 0.021 0.001 TYR A 998 PHE 0.011 0.001 PHE A 817 TRP 0.009 0.001 TRP A2221 HIS 0.004 0.001 HIS A2352 Details of bonding type rmsd covalent geometry : bond 0.00281 (10584) covalent geometry : angle 0.46150 (14447) hydrogen bonds : bond 0.04048 ( 693) hydrogen bonds : angle 3.23614 ( 2043) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2653.81 seconds wall clock time: 46 minutes 2.60 seconds (2762.60 seconds total)