Starting phenix.real_space_refine on Mon Jun 9 12:57:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6or5_9032/06_2025/6or5_9032.cif Found real_map, /net/cci-nas-00/data/ceres_data/6or5_9032/06_2025/6or5_9032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6or5_9032/06_2025/6or5_9032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6or5_9032/06_2025/6or5_9032.map" model { file = "/net/cci-nas-00/data/ceres_data/6or5_9032/06_2025/6or5_9032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6or5_9032/06_2025/6or5_9032.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.030 sd= 0.761 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians P 15 5.49 5 C 6143 2.51 5 N 2088 2.21 5 O 2118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10364 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2058, 10209 Classifications: {'peptide': 2058} Incomplete info: {'truncation_to_alanine': 1855} Link IDs: {'PTRANS': 74, 'TRANS': 1983} Chain breaks: 55 Unresolved chain link angles: 74 Unresolved non-hydrogen bonds: 6745 Unresolved non-hydrogen angles: 8670 Unresolved non-hydrogen dihedrals: 5586 Unresolved non-hydrogen chiralities: 687 Planarities with less than four sites: {'GLN:plan1': 79, 'ARG:plan': 110, 'TYR:plan': 67, 'ASN:plan1': 97, 'TRP:plan': 27, 'HIS:plan': 53, 'PHE:plan': 98, 'GLU:plan': 145, 'ASP:plan': 95} Unresolved non-hydrogen planarities: 3587 Chain: "A" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 155 Unusual residues: {'ANP': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 7.75, per 1000 atoms: 0.75 Number of scatterers: 10364 At special positions: 0 Unit cell: (136.5, 172.9, 110.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 15 15.00 O 2118 8.00 N 2088 7.00 C 6143 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: 3.05 Conformation dependent library (CDL) restraints added in 2.0 seconds 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 7 sheets defined 56.8% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 13 through 22 removed outlier: 3.525A pdb=" N ASN A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 33 Processing helix chain 'A' and resid 45 through 50 removed outlier: 4.532A pdb=" N ALA A 50 " --> pdb=" O TRP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 58 removed outlier: 3.778A pdb=" N CYS A 58 " --> pdb=" O ARG A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.578A pdb=" N LEU A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 136 through 152 Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 164 through 176 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 291 through 300 removed outlier: 3.593A pdb=" N VAL A 297 " --> pdb=" O CYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 304 Processing helix chain 'A' and resid 306 through 323 Processing helix chain 'A' and resid 338 through 353 Processing helix chain 'A' and resid 374 through 381 removed outlier: 3.617A pdb=" N ILE A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 402 Processing helix chain 'A' and resid 408 through 412 removed outlier: 3.522A pdb=" N GLN A 411 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 412 " --> pdb=" O ALA A 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 408 through 412' Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.711A pdb=" N THR A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 491 Processing helix chain 'A' and resid 505 through 510 removed outlier: 3.962A pdb=" N MET A 509 " --> pdb=" O GLU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 537 removed outlier: 3.846A pdb=" N LEU A 525 " --> pdb=" O LEU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.650A pdb=" N ALA A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 575 removed outlier: 3.764A pdb=" N ALA A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 616 Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 654 through 663 removed outlier: 3.967A pdb=" N SER A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.840A pdb=" N SER A 728 " --> pdb=" O ASP A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 757 Processing helix chain 'A' and resid 758 through 760 No H-bonds generated for 'chain 'A' and resid 758 through 760' Processing helix chain 'A' and resid 777 through 789 Processing helix chain 'A' and resid 795 through 806 removed outlier: 3.586A pdb=" N SER A 806 " --> pdb=" O GLY A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 828 Processing helix chain 'A' and resid 833 through 840 Processing helix chain 'A' and resid 877 through 891 Processing helix chain 'A' and resid 906 through 916 Processing helix chain 'A' and resid 932 through 937 removed outlier: 3.673A pdb=" N TYR A 936 " --> pdb=" O ASP A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 961 removed outlier: 3.528A pdb=" N ALA A 958 " --> pdb=" O VAL A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 973 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 1027 through 1031 Processing helix chain 'A' and resid 1041 through 1053 removed outlier: 3.707A pdb=" N HIS A1050 " --> pdb=" O GLU A1046 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS A1051 " --> pdb=" O THR A1047 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A1052 " --> pdb=" O ILE A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1074 removed outlier: 4.032A pdb=" N ARG A1074 " --> pdb=" O LEU A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1099 Processing helix chain 'A' and resid 1103 through 1116 Processing helix chain 'A' and resid 1121 through 1135 removed outlier: 3.549A pdb=" N MET A1135 " --> pdb=" O ILE A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1186 removed outlier: 3.817A pdb=" N ARG A1174 " --> pdb=" O ARG A1170 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU A1175 " --> pdb=" O PRO A1171 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU A1178 " --> pdb=" O ARG A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1210 Processing helix chain 'A' and resid 1226 through 1231 removed outlier: 4.017A pdb=" N GLY A1230 " --> pdb=" O GLY A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1249 removed outlier: 3.698A pdb=" N ASN A1242 " --> pdb=" O ARG A1238 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU A1245 " --> pdb=" O VAL A1241 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS A1246 " --> pdb=" O ASN A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1272 removed outlier: 3.683A pdb=" N LEU A1272 " --> pdb=" O LYS A1268 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1290 Processing helix chain 'A' and resid 1301 through 1309 Processing helix chain 'A' and resid 1317 through 1321 Processing helix chain 'A' and resid 1323 through 1334 removed outlier: 3.906A pdb=" N GLU A1334 " --> pdb=" O ASN A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1375 through 1381 Processing helix chain 'A' and resid 1394 through 1404 Processing helix chain 'A' and resid 1411 through 1426 removed outlier: 3.950A pdb=" N GLU A1417 " --> pdb=" O ARG A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1446 removed outlier: 3.595A pdb=" N VAL A1437 " --> pdb=" O SER A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1451 through 1463 Processing helix chain 'A' and resid 1481 through 1498 Processing helix chain 'A' and resid 1543 through 1557 removed outlier: 3.728A pdb=" N GLN A1557 " --> pdb=" O LEU A1553 " (cutoff:3.500A) Processing helix chain 'A' and resid 1572 through 1577 Processing helix chain 'A' and resid 1598 through 1603 Processing helix chain 'A' and resid 1622 through 1629 Processing helix chain 'A' and resid 1637 through 1641 Processing helix chain 'A' and resid 1644 through 1653 Processing helix chain 'A' and resid 1709 through 1718 Processing helix chain 'A' and resid 1725 through 1744 Processing helix chain 'A' and resid 1759 through 1771 removed outlier: 3.602A pdb=" N ASN A1771 " --> pdb=" O LEU A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1788 Processing helix chain 'A' and resid 1795 through 1811 Processing helix chain 'A' and resid 1852 through 1854 No H-bonds generated for 'chain 'A' and resid 1852 through 1854' Processing helix chain 'A' and resid 1855 through 1868 removed outlier: 3.654A pdb=" N GLU A1860 " --> pdb=" O LEU A1856 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER A1861 " --> pdb=" O PRO A1857 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS A1865 " --> pdb=" O SER A1861 " (cutoff:3.500A) Processing helix chain 'A' and resid 1882 through 1894 Processing helix chain 'A' and resid 1907 through 1912 Processing helix chain 'A' and resid 1920 through 1942 removed outlier: 3.808A pdb=" N LYS A1941 " --> pdb=" O ASN A1937 " (cutoff:3.500A) Processing helix chain 'A' and resid 1949 through 1958 Processing helix chain 'A' and resid 1969 through 1980 removed outlier: 3.680A pdb=" N GLN A1973 " --> pdb=" O PHE A1969 " (cutoff:3.500A) Processing helix chain 'A' and resid 1987 through 2003 removed outlier: 4.279A pdb=" N ILE A1995 " --> pdb=" O SER A1991 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS A1998 " --> pdb=" O ASP A1994 " (cutoff:3.500A) Processing helix chain 'A' and resid 2004 through 2006 No H-bonds generated for 'chain 'A' and resid 2004 through 2006' Processing helix chain 'A' and resid 2020 through 2025 removed outlier: 3.926A pdb=" N ALA A2024 " --> pdb=" O TYR A2020 " (cutoff:3.500A) Processing helix chain 'A' and resid 2040 through 2052 removed outlier: 3.854A pdb=" N LEU A2044 " --> pdb=" O SER A2040 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A2050 " --> pdb=" O ARG A2046 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A2052 " --> pdb=" O ASN A2048 " (cutoff:3.500A) Processing helix chain 'A' and resid 2092 through 2097 Processing helix chain 'A' and resid 2109 through 2117 removed outlier: 3.563A pdb=" N MET A2117 " --> pdb=" O ASP A2113 " (cutoff:3.500A) Processing helix chain 'A' and resid 2130 through 2143 removed outlier: 4.055A pdb=" N ILE A2136 " --> pdb=" O LEU A2132 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A2143 " --> pdb=" O ILE A2139 " (cutoff:3.500A) Processing helix chain 'A' and resid 2155 through 2167 removed outlier: 4.176A pdb=" N ALA A2159 " --> pdb=" O TYR A2155 " (cutoff:3.500A) Processing helix chain 'A' and resid 2168 through 2178 Processing helix chain 'A' and resid 2199 through 2214 removed outlier: 3.787A pdb=" N GLN A2204 " --> pdb=" O LYS A2200 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS A2205 " --> pdb=" O ASN A2201 " (cutoff:3.500A) Processing helix chain 'A' and resid 2217 through 2228 Processing helix chain 'A' and resid 2238 through 2245 removed outlier: 3.515A pdb=" N PHE A2245 " --> pdb=" O THR A2241 " (cutoff:3.500A) Processing helix chain 'A' and resid 2254 through 2280 removed outlier: 3.928A pdb=" N THR A2259 " --> pdb=" O GLU A2255 " (cutoff:3.500A) Processing helix chain 'A' and resid 2291 through 2298 Processing helix chain 'A' and resid 2312 through 2329 removed outlier: 4.177A pdb=" N PHE A2320 " --> pdb=" O LEU A2316 " (cutoff:3.500A) Processing helix chain 'A' and resid 2333 through 2337 Processing helix chain 'A' and resid 2342 through 2360 Processing helix chain 'A' and resid 2369 through 2383 Processing helix chain 'A' and resid 2390 through 2407 Proline residue: A2396 - end of helix Processing helix chain 'A' and resid 2759 through 2783 removed outlier: 4.101A pdb=" N LEU A2781 " --> pdb=" O ILE A2777 " (cutoff:3.500A) Processing helix chain 'A' and resid 2788 through 2800 removed outlier: 3.889A pdb=" N ASN A2800 " --> pdb=" O THR A2796 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 182 through 184 Processing sheet with id=AA2, first strand: chain 'A' and resid 495 through 496 removed outlier: 5.827A pdb=" N TRP A 641 " --> pdb=" O THR A 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 923 through 926 removed outlier: 6.625A pdb=" N VAL A 923 " --> pdb=" O VAL A 966 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP A 968 " --> pdb=" O VAL A 923 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE A 925 " --> pdb=" O ASP A 968 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 967 " --> pdb=" O LEU A1008 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA A1010 " --> pdb=" O LEU A 967 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1215 through 1218 removed outlier: 7.308A pdb=" N HIS A1215 " --> pdb=" O LEU A1314 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASP A1316 " --> pdb=" O HIS A1215 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE A1217 " --> pdb=" O ASP A1316 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1587 through 1591 removed outlier: 6.158A pdb=" N ILE A1562 " --> pdb=" O ALA A1678 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU A1563 " --> pdb=" O VAL A1703 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1822 through 1823 Processing sheet with id=AA7, first strand: chain 'A' and resid 1897 through 1901 removed outlier: 6.429A pdb=" N LYS A1898 " --> pdb=" O VAL A2032 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP A2034 " --> pdb=" O LYS A1898 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N MET A1900 " --> pdb=" O ASP A2034 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE A2031 " --> pdb=" O PHE A2081 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N THR A2083 " --> pdb=" O PHE A2031 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU A2033 " --> pdb=" O THR A2083 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N CYS A1872 " --> pdb=" O LEU A2082 " (cutoff:3.500A) 724 hydrogen bonds defined for protein. 2124 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: 5.06 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.31: 2071 1.31 - 1.41: 2045 1.41 - 1.50: 2115 1.50 - 1.60: 4077 1.60 - 1.69: 10 Bond restraints: 10318 Sorted by residual: bond pdb=" O3A ANP A7204 " pdb=" PB ANP A7204 " ideal model delta sigma weight residual 1.700 1.534 0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" O3A ANP A7203 " pdb=" PB ANP A7203 " ideal model delta sigma weight residual 1.700 1.541 0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" O3A ANP A7201 " pdb=" PB ANP A7201 " ideal model delta sigma weight residual 1.700 1.541 0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" O3A ANP A7205 " pdb=" PB ANP A7205 " ideal model delta sigma weight residual 1.700 1.545 0.155 2.00e-02 2.50e+03 6.02e+01 bond pdb=" O3A ANP A7202 " pdb=" PB ANP A7202 " ideal model delta sigma weight residual 1.700 1.562 0.138 2.00e-02 2.50e+03 4.74e+01 ... (remaining 10313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.31: 14259 5.31 - 10.61: 63 10.61 - 15.92: 9 15.92 - 21.22: 2 21.22 - 26.53: 3 Bond angle restraints: 14336 Sorted by residual: angle pdb=" PB ANP A7201 " pdb=" N3B ANP A7201 " pdb=" PG ANP A7201 " ideal model delta sigma weight residual 126.95 100.42 26.53 3.00e+00 1.11e-01 7.82e+01 angle pdb=" PB ANP A7205 " pdb=" N3B ANP A7205 " pdb=" PG ANP A7205 " ideal model delta sigma weight residual 126.95 101.31 25.64 3.00e+00 1.11e-01 7.31e+01 angle pdb=" PB ANP A7204 " pdb=" N3B ANP A7204 " pdb=" PG ANP A7204 " ideal model delta sigma weight residual 126.95 103.33 23.62 3.00e+00 1.11e-01 6.20e+01 angle pdb=" N ILE A1055 " pdb=" CA ILE A1055 " pdb=" C ILE A1055 " ideal model delta sigma weight residual 108.17 119.01 -10.84 1.40e+00 5.10e-01 5.99e+01 angle pdb=" PA ANP A7205 " pdb=" O3A ANP A7205 " pdb=" PB ANP A7205 " ideal model delta sigma weight residual 125.41 107.68 17.73 3.00e+00 1.11e-01 3.49e+01 ... (remaining 14331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 6037 35.14 - 70.29: 46 70.29 - 105.43: 29 105.43 - 140.58: 3 140.58 - 175.72: 1 Dihedral angle restraints: 6116 sinusoidal: 160 harmonic: 5956 Sorted by residual: dihedral pdb=" CA HIS A 424 " pdb=" C HIS A 424 " pdb=" N ASN A 425 " pdb=" CA ASN A 425 " ideal model delta harmonic sigma weight residual 180.00 -150.35 -29.65 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA ILE A1661 " pdb=" C ILE A1661 " pdb=" N PRO A1662 " pdb=" CA PRO A1662 " ideal model delta harmonic sigma weight residual -180.00 -151.67 -28.33 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA GLY A 794 " pdb=" C GLY A 794 " pdb=" N LEU A 795 " pdb=" CA LEU A 795 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 6113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1682 0.066 - 0.132: 286 0.132 - 0.198: 22 0.198 - 0.263: 5 0.263 - 0.329: 2 Chirality restraints: 1997 Sorted by residual: chirality pdb=" C3' ANP A7202 " pdb=" C2' ANP A7202 " pdb=" C4' ANP A7202 " pdb=" O3' ANP A7202 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C3' ANP A7204 " pdb=" C2' ANP A7204 " pdb=" C4' ANP A7204 " pdb=" O3' ANP A7204 " both_signs ideal model delta sigma weight residual False -2.36 -2.67 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" C3' ANP A7203 " pdb=" C2' ANP A7203 " pdb=" C4' ANP A7203 " pdb=" O3' ANP A7203 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 1994 not shown) Planarity restraints: 2007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A2223 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C MET A2223 " -0.063 2.00e-02 2.50e+03 pdb=" O MET A2223 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP A2224 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 46 " -0.012 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C TRP A 46 " 0.039 2.00e-02 2.50e+03 pdb=" O TRP A 46 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE A 47 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 54 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C ILE A 54 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE A 54 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 55 " 0.012 2.00e-02 2.50e+03 ... (remaining 2004 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2780 2.78 - 3.31: 10352 3.31 - 3.84: 15288 3.84 - 4.37: 15546 4.37 - 4.90: 24049 Nonbonded interactions: 68015 Sorted by model distance: nonbonded pdb=" O2B ANP A7205 " pdb=" O2G ANP A7205 " model vdw 2.245 3.040 nonbonded pdb=" O1B ANP A7201 " pdb=" O2A ANP A7201 " model vdw 2.261 3.040 nonbonded pdb=" O ALA A 50 " pdb=" CB ARG A 55 " model vdw 2.264 3.440 nonbonded pdb=" O PHE A2222 " pdb=" CB TYR A2226 " model vdw 2.282 2.752 nonbonded pdb=" C ALA A1659 " pdb=" O ASP A1665 " model vdw 2.282 3.270 ... (remaining 68010 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.780 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.166 10318 Z= 0.464 Angle : 1.123 26.527 14336 Z= 0.624 Chirality : 0.050 0.329 1997 Planarity : 0.005 0.037 2007 Dihedral : 15.946 175.724 2162 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 17.32 % Favored : 82.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.53 (0.14), residues: 1946 helix: -2.84 (0.11), residues: 1059 sheet: -4.87 (0.34), residues: 102 loop : -4.63 (0.18), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 7 PHE 0.000 0.000 PHE A 47 TYR 0.000 0.000 TYR A 11 Details of bonding type rmsd hydrogen bonds : bond 0.18340 ( 724) hydrogen bonds : angle 8.18329 ( 2124) covalent geometry : bond 0.00758 (10318) covalent geometry : angle 1.12293 (14336) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0940 time to fit residues: 8.0215 Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.1980 chunk 155 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 104 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 160 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 186 optimal weight: 2.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.053584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.046460 restraints weight = 92800.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.047063 restraints weight = 67164.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.047518 restraints weight = 52265.963| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 10318 Z= 0.146 Angle : 0.557 10.053 14336 Z= 0.321 Chirality : 0.040 0.139 1997 Planarity : 0.002 0.024 2007 Dihedral : 11.947 169.594 2162 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 0.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.51 % Favored : 86.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.17), residues: 1946 helix: -0.77 (0.14), residues: 1126 sheet: -4.70 (0.35), residues: 101 loop : -4.58 (0.19), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 7 PHE 0.000 0.000 PHE A 47 TYR 0.000 0.000 TYR A 11 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 724) hydrogen bonds : angle 5.26757 ( 2124) covalent geometry : bond 0.00205 (10318) covalent geometry : angle 0.55688 (14336) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.052 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1005 time to fit residues: 8.4205 Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 33 optimal weight: 0.0970 chunk 110 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 chunk 156 optimal weight: 0.0770 chunk 7 optimal weight: 7.9990 chunk 169 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 overall best weight: 1.2338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.054930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.047586 restraints weight = 92887.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.048222 restraints weight = 67732.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.048696 restraints weight = 52690.668| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.011 10318 Z= 0.087 Angle : 0.438 5.725 14336 Z= 0.253 Chirality : 0.038 0.135 1997 Planarity : 0.002 0.014 2007 Dihedral : 9.931 173.342 2162 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.20), residues: 1946 helix: 0.69 (0.16), residues: 1129 sheet: -4.50 (0.38), residues: 102 loop : -4.34 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 7 PHE 0.000 0.000 PHE A 47 TYR 0.000 0.000 TYR A 11 Details of bonding type rmsd hydrogen bonds : bond 0.02802 ( 724) hydrogen bonds : angle 4.19873 ( 2124) covalent geometry : bond 0.00122 (10318) covalent geometry : angle 0.43816 (14336) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.069 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0918 time to fit residues: 7.7347 Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 176 optimal weight: 20.0000 chunk 151 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 174 optimal weight: 20.0000 chunk 139 optimal weight: 40.0000 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 76 optimal weight: 30.0000 chunk 26 optimal weight: 8.9990 chunk 114 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.051909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.044959 restraints weight = 95079.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.045511 restraints weight = 69512.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.045921 restraints weight = 54561.436| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10318 Z= 0.320 Angle : 0.674 11.777 14336 Z= 0.404 Chirality : 0.042 0.151 1997 Planarity : 0.003 0.020 2007 Dihedral : 10.757 169.264 2162 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.88 % Favored : 82.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.19), residues: 1946 helix: -0.08 (0.15), residues: 1120 sheet: -4.55 (0.38), residues: 101 loop : -4.49 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 7 PHE 0.000 0.000 PHE A 47 TYR 0.000 0.000 TYR A 11 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 724) hydrogen bonds : angle 5.73624 ( 2124) covalent geometry : bond 0.00457 (10318) covalent geometry : angle 0.67353 (14336) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.180 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0960 time to fit residues: 8.2443 Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 188 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 199 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 9 optimal weight: 0.0470 chunk 32 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 103 optimal weight: 0.0030 chunk 178 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 overall best weight: 4.2094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.052782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.045683 restraints weight = 93434.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.046258 restraints weight = 68138.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.046705 restraints weight = 53248.263| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10318 Z= 0.199 Angle : 0.549 9.116 14336 Z= 0.323 Chirality : 0.040 0.130 1997 Planarity : 0.002 0.019 2007 Dihedral : 10.382 171.514 2162 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.31 % Favored : 84.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.19), residues: 1946 helix: 0.33 (0.16), residues: 1125 sheet: -4.43 (0.39), residues: 107 loop : -4.42 (0.20), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 7 PHE 0.000 0.000 PHE A 47 TYR 0.000 0.000 TYR A 11 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 724) hydrogen bonds : angle 5.06315 ( 2124) covalent geometry : bond 0.00284 (10318) covalent geometry : angle 0.54888 (14336) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.188 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0985 time to fit residues: 8.4771 Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 119 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.052808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.045665 restraints weight = 93841.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.046250 restraints weight = 68249.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.046692 restraints weight = 53274.519| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10318 Z= 0.200 Angle : 0.541 8.463 14336 Z= 0.319 Chirality : 0.040 0.132 1997 Planarity : 0.002 0.016 2007 Dihedral : 10.185 173.616 2162 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.27 % Favored : 82.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.20), residues: 1946 helix: 0.53 (0.16), residues: 1126 sheet: -4.60 (0.39), residues: 108 loop : -4.33 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 7 PHE 0.000 0.000 PHE A 47 TYR 0.000 0.000 TYR A 11 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 724) hydrogen bonds : angle 4.96676 ( 2124) covalent geometry : bond 0.00287 (10318) covalent geometry : angle 0.54137 (14336) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.077 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0915 time to fit residues: 7.7292 Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 93 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 45 optimal weight: 30.0000 chunk 71 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 108 optimal weight: 40.0000 chunk 67 optimal weight: 0.6980 overall best weight: 6.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.052016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.044959 restraints weight = 96848.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.045546 restraints weight = 69966.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.045983 restraints weight = 54411.052| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10318 Z= 0.308 Angle : 0.660 11.207 14336 Z= 0.394 Chirality : 0.041 0.145 1997 Planarity : 0.003 0.019 2007 Dihedral : 10.634 173.739 2162 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 19.27 % Favored : 80.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.19), residues: 1946 helix: -0.16 (0.15), residues: 1121 sheet: -4.31 (0.45), residues: 93 loop : -4.47 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 7 PHE 0.000 0.000 PHE A 47 TYR 0.000 0.000 TYR A 11 Details of bonding type rmsd hydrogen bonds : bond 0.04540 ( 724) hydrogen bonds : angle 5.76650 ( 2124) covalent geometry : bond 0.00440 (10318) covalent geometry : angle 0.65960 (14336) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.094 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0930 time to fit residues: 7.9592 Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 69 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 24 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 152 optimal weight: 0.3980 overall best weight: 8.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.051453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.044536 restraints weight = 96019.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.045106 restraints weight = 69274.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.045530 restraints weight = 53553.304| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10318 Z= 0.365 Angle : 0.729 12.415 14336 Z= 0.437 Chirality : 0.043 0.151 1997 Planarity : 0.004 0.020 2007 Dihedral : 10.964 172.558 2162 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 21.02 % Favored : 78.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.18), residues: 1946 helix: -0.77 (0.15), residues: 1120 sheet: -4.36 (0.45), residues: 93 loop : -4.59 (0.19), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 7 PHE 0.000 0.000 PHE A 47 TYR 0.000 0.000 TYR A 11 Details of bonding type rmsd hydrogen bonds : bond 0.05080 ( 724) hydrogen bonds : angle 6.26071 ( 2124) covalent geometry : bond 0.00523 (10318) covalent geometry : angle 0.72912 (14336) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.244 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0979 time to fit residues: 8.4531 Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 67 optimal weight: 8.9990 chunk 199 optimal weight: 3.9990 chunk 160 optimal weight: 20.0000 chunk 194 optimal weight: 20.0000 chunk 117 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 45 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 61 optimal weight: 0.0020 chunk 123 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.053777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.046509 restraints weight = 94284.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.047130 restraints weight = 68509.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.047603 restraints weight = 53057.738| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 10318 Z= 0.103 Angle : 0.458 5.713 14336 Z= 0.264 Chirality : 0.039 0.132 1997 Planarity : 0.002 0.015 2007 Dihedral : 9.948 176.394 2162 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.20), residues: 1946 helix: 0.95 (0.16), residues: 1111 sheet: -4.32 (0.45), residues: 100 loop : -4.10 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 7 PHE 0.000 0.000 PHE A 47 TYR 0.000 0.000 TYR A 11 Details of bonding type rmsd hydrogen bonds : bond 0.02979 ( 724) hydrogen bonds : angle 4.40912 ( 2124) covalent geometry : bond 0.00145 (10318) covalent geometry : angle 0.45818 (14336) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.166 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0984 time to fit residues: 8.4562 Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 12 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 180 optimal weight: 8.9990 chunk 162 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 128 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 166 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.053004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.045838 restraints weight = 94447.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.046430 restraints weight = 68660.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.046881 restraints weight = 53562.062| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10318 Z= 0.167 Angle : 0.500 7.225 14336 Z= 0.293 Chirality : 0.039 0.135 1997 Planarity : 0.002 0.014 2007 Dihedral : 9.974 177.981 2162 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.14 % Favored : 83.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.20), residues: 1946 helix: 0.98 (0.16), residues: 1118 sheet: -4.11 (0.48), residues: 94 loop : -4.20 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 7 PHE 0.000 0.000 PHE A 47 TYR 0.000 0.000 TYR A 11 Details of bonding type rmsd hydrogen bonds : bond 0.03321 ( 724) hydrogen bonds : angle 4.66098 ( 2124) covalent geometry : bond 0.00238 (10318) covalent geometry : angle 0.49981 (14336) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.066 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0953 time to fit residues: 8.0558 Evaluate side-chains 36 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 203 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 126 optimal weight: 0.0040 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 201 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.054117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.046852 restraints weight = 92935.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.047461 restraints weight = 67658.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.047920 restraints weight = 52701.288| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.012 10318 Z= 0.104 Angle : 0.435 5.044 14336 Z= 0.252 Chirality : 0.038 0.135 1997 Planarity : 0.002 0.014 2007 Dihedral : 9.580 178.749 2162 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.82 % Favored : 88.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.21), residues: 1946 helix: 1.49 (0.17), residues: 1126 sheet: -3.95 (0.49), residues: 94 loop : -3.96 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 7 PHE 0.000 0.000 PHE A 47 TYR 0.000 0.000 TYR A 11 Details of bonding type rmsd hydrogen bonds : bond 0.02732 ( 724) hydrogen bonds : angle 4.04457 ( 2124) covalent geometry : bond 0.00147 (10318) covalent geometry : angle 0.43467 (14336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2930.28 seconds wall clock time: 50 minutes 51.98 seconds (3051.98 seconds total)