Starting phenix.real_space_refine on Wed Sep 25 15:24:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6or5_9032/09_2024/6or5_9032.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6or5_9032/09_2024/6or5_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6or5_9032/09_2024/6or5_9032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6or5_9032/09_2024/6or5_9032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6or5_9032/09_2024/6or5_9032.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6or5_9032/09_2024/6or5_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-5461/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: 7.58, per 1000 atoms: 0.73 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: 3.19 Conformation dependent library (CDL) restraints added in 2.1 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: 1.66 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: 5.51 Time building geometry restraints manager: 3.63 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: 2.320 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.310 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.260 ------------------------------------------------------------------------------- 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= 0.558 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.293 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0942 time to fit residues: 8.2502 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 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= 0.149 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.954 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0979 time to fit residues: 8.2788 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 186 optimal weight: 9.9990 chunk 201 optimal weight: 0.0970 chunk 166 optimal weight: 9.9990 chunk 184 optimal weight: 40.0000 chunk 63 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 overall best weight: 6.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10318 Z= 0.304 Angle : 0.678 12.512 14336 Z= 0.403 Chirality : 0.041 0.176 1997 Planarity : 0.003 0.025 2007 Dihedral : 11.238 166.744 2162 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 18.71 % Favored : 81.24 % 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: -3.26 (0.18), residues: 1946 helix: -0.50 (0.15), residues: 1120 sheet: -4.63 (0.37), residues: 103 loop : -4.57 (0.20), residues: 723 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.209 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1022 time to fit residues: 8.7015 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 30.0000 chunk 140 optimal weight: 7.9990 chunk 96 optimal weight: 0.1980 chunk 20 optimal weight: 20.0000 chunk 89 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 177 optimal weight: 8.9990 chunk 53 optimal weight: 0.0070 overall best weight: 2.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 10318 Z= 0.142 Angle : 0.495 7.213 14336 Z= 0.288 Chirality : 0.039 0.131 1997 Planarity : 0.002 0.017 2007 Dihedral : 10.240 168.888 2162 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 0.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.46 % Favored : 86.54 % 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: -2.25 (0.20), residues: 1946 helix: 0.47 (0.16), residues: 1123 sheet: -4.53 (0.39), residues: 102 loop : -4.41 (0.20), residues: 721 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.172 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0946 time to fit residues: 8.0927 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 0.0870 chunk 112 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 169 optimal weight: 20.0000 chunk 136 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 177 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 overall best weight: 4.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10318 Z= 0.208 Angle : 0.543 8.566 14336 Z= 0.320 Chirality : 0.040 0.132 1997 Planarity : 0.002 0.017 2007 Dihedral : 10.284 171.213 2162 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 1.21 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: -2.19 (0.20), residues: 1946 helix: 0.49 (0.16), residues: 1123 sheet: -4.52 (0.40), residues: 102 loop : -4.33 (0.21), residues: 721 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.255 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0929 time to fit residues: 8.1190 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 8.9990 chunk 178 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 164 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 104 optimal weight: 0.0470 overall best weight: 2.2684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 10318 Z= 0.117 Angle : 0.454 5.851 14336 Z= 0.263 Chirality : 0.039 0.133 1997 Planarity : 0.002 0.014 2007 Dihedral : 9.827 173.847 2162 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.59 % Favored : 87.41 % 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: -1.46 (0.20), residues: 1946 helix: 1.16 (0.16), residues: 1121 sheet: -4.25 (0.41), residues: 107 loop : -4.13 (0.21), residues: 718 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.169 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0970 time to fit residues: 8.3499 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 112 optimal weight: 0.6980 chunk 166 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 chunk 120 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 overall best weight: 5.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10318 Z= 0.270 Angle : 0.601 9.661 14336 Z= 0.357 Chirality : 0.041 0.144 1997 Planarity : 0.003 0.017 2007 Dihedral : 10.340 174.204 2162 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.65 % Favored : 81.35 % 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: -2.20 (0.20), residues: 1946 helix: 0.43 (0.16), residues: 1122 sheet: -4.26 (0.45), residues: 93 loop : -4.29 (0.21), residues: 731 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.274 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1007 time to fit residues: 8.6907 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 134 optimal weight: 30.0000 chunk 97 optimal weight: 10.0000 chunk 18 optimal weight: 30.0000 chunk 155 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2509 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= 0.363 Angle : 0.707 12.217 14336 Z= 0.424 Chirality : 0.042 0.152 1997 Planarity : 0.004 0.019 2007 Dihedral : 10.811 173.692 2162 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 19.68 % Favored : 80.27 % 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: -3.13 (0.18), residues: 1946 helix: -0.45 (0.15), residues: 1120 sheet: -4.30 (0.45), residues: 93 loop : -4.49 (0.20), 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.291 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0965 time to fit residues: 8.4379 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 7.9990 chunk 172 optimal weight: 30.0000 chunk 184 optimal weight: 30.0000 chunk 110 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 166 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 183 optimal weight: 0.4980 chunk 120 optimal weight: 20.0000 overall best weight: 6.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10318 Z= 0.295 Angle : 0.637 10.710 14336 Z= 0.379 Chirality : 0.041 0.144 1997 Planarity : 0.003 0.018 2007 Dihedral : 10.645 173.939 2162 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 19.89 % Favored : 80.06 % 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: -3.04 (0.18), residues: 1946 helix: -0.36 (0.15), residues: 1121 sheet: -4.34 (0.46), residues: 94 loop : -4.48 (0.20), residues: 731 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.253 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0937 time to fit residues: 8.0799 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 135 optimal weight: 30.0000 chunk 204 optimal weight: 7.9990 chunk 187 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 125 optimal weight: 8.9990 chunk 99 optimal weight: 0.7980 chunk 129 optimal weight: 8.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10318 Z= 0.200 Angle : 0.539 8.211 14336 Z= 0.317 Chirality : 0.040 0.130 1997 Planarity : 0.002 0.015 2007 Dihedral : 10.274 176.181 2162 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.50 % Favored : 83.50 % 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: -2.34 (0.19), residues: 1946 helix: 0.32 (0.16), residues: 1117 sheet: -4.24 (0.47), residues: 94 loop : -4.33 (0.20), 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 ********************** 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 fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.232 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0974 time to fit residues: 8.3104 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 45 optimal weight: 30.0000 chunk 162 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 167 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- 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 = 0.3214 r_free = 0.3214 target = 0.052201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.045169 restraints weight = 94624.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.045742 restraints weight = 68756.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.046178 restraints weight = 53666.156| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10318 Z= 0.262 Angle : 0.591 9.253 14336 Z= 0.352 Chirality : 0.041 0.138 1997 Planarity : 0.003 0.015 2007 Dihedral : 10.417 176.477 2162 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.17 % Favored : 80.83 % 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: -2.56 (0.19), residues: 1946 helix: 0.11 (0.16), residues: 1120 sheet: -4.26 (0.46), residues: 94 loop : -4.41 (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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1507.37 seconds wall clock time: 27 minutes 21.61 seconds (1641.61 seconds total)