Starting phenix.real_space_refine on Sat Dec 9 07:21:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6or5_9032/12_2023/6or5_9032_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6or5_9032/12_2023/6or5_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_9032/12_2023/6or5_9032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6or5_9032/12_2023/6or5_9032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6or5_9032/12_2023/6or5_9032_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6or5_9032/12_2023/6or5_9032_updated.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10364 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2063, 10364 Unusual residues: {'ANP': 5} Classifications: {'peptide': 2058, 'undetermined': 5} Incomplete info: {'truncation_to_alanine': 1855} Link IDs: {'PTRANS': 74, 'TRANS': 1983, None: 5} Not linked: pdbres="ASN A2800 " pdbres="ANP A7201 " Not linked: pdbres="ANP A7201 " pdbres="ANP A7202 " Not linked: pdbres="ANP A7202 " pdbres="ANP A7203 " Not linked: pdbres="ANP A7203 " pdbres="ANP A7204 " Not linked: pdbres="ANP A7204 " pdbres="ANP A7205 " 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 Time building chain proxies: 6.32, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 4.19 Conformation dependent library (CDL) restraints added in 2.8 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... running ksdssp... Secondary structure from input PDB file: 101 helices and 6 sheets defined 49.8% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.23 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 46 through 49 No H-bonds generated for 'chain 'A' and resid 46 through 49' Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 79 through 88 removed outlier: 3.578A pdb=" N LEU A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 88 " --> pdb=" O HIS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 137 through 151 Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 165 through 175 Processing helix chain 'A' and resid 192 through 195 No H-bonds generated for 'chain 'A' and resid 192 through 195' Processing helix chain 'A' and resid 213 through 219 Processing helix chain 'A' and resid 235 through 244 Proline residue: A 241 - end of helix Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 289 through 299 removed outlier: 4.267A pdb=" N VAL A 296 " --> pdb=" O CYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 303 No H-bonds generated for 'chain 'A' and resid 301 through 303' Processing helix chain 'A' and resid 307 through 322 Processing helix chain 'A' and resid 339 through 352 Processing helix chain 'A' and resid 375 through 382 Processing helix chain 'A' and resid 388 through 401 Processing helix chain 'A' and resid 407 through 411 removed outlier: 3.590A pdb=" N GLN A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 407 through 411' Processing helix chain 'A' and resid 451 through 464 Processing helix chain 'A' and resid 479 through 490 Processing helix chain 'A' and resid 506 through 509 No H-bonds generated for 'chain 'A' and resid 506 through 509' Processing helix chain 'A' and resid 521 through 536 removed outlier: 3.846A pdb=" N LEU A 525 " --> pdb=" O LEU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'A' and resid 561 through 574 removed outlier: 3.764A pdb=" N ALA A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 615 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 725 through 734 Processing helix chain 'A' and resid 742 through 759 removed outlier: 5.234A pdb=" N SER A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 788 Processing helix chain 'A' and resid 796 through 805 Processing helix chain 'A' and resid 815 through 827 Processing helix chain 'A' and resid 833 through 839 Processing helix chain 'A' and resid 843 through 846 No H-bonds generated for 'chain 'A' and resid 843 through 846' Processing helix chain 'A' and resid 878 through 890 Processing helix chain 'A' and resid 907 through 916 Processing helix chain 'A' and resid 933 through 936 No H-bonds generated for 'chain 'A' and resid 933 through 936' Processing helix chain 'A' and resid 955 through 960 Processing helix chain 'A' and resid 970 through 972 No H-bonds generated for 'chain 'A' and resid 970 through 972' Processing helix chain 'A' and resid 977 through 984 Processing helix chain 'A' and resid 1028 through 1030 No H-bonds generated for 'chain 'A' and resid 1028 through 1030' Processing helix chain 'A' and resid 1042 through 1052 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 1059 through 1073 Processing helix chain 'A' and resid 1089 through 1098 Processing helix chain 'A' and resid 1104 through 1115 Processing helix chain 'A' and resid 1122 through 1134 Processing helix chain 'A' and resid 1170 through 1185 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 1199 through 1209 Processing helix chain 'A' and resid 1225 through 1230 removed outlier: 4.017A pdb=" N GLY A1230 " --> pdb=" O GLY A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1249 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 1271 Processing helix chain 'A' and resid 1284 through 1288 Processing helix chain 'A' and resid 1302 through 1308 Processing helix chain 'A' and resid 1318 through 1320 No H-bonds generated for 'chain 'A' and resid 1318 through 1320' Processing helix chain 'A' and resid 1324 through 1331 Processing helix chain 'A' and resid 1376 through 1380 Processing helix chain 'A' and resid 1394 through 1403 Processing helix chain 'A' and resid 1410 through 1425 Proline residue: A1414 - end of helix removed outlier: 3.950A pdb=" N GLU A1417 " --> pdb=" O ARG A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1445 Processing helix chain 'A' and resid 1452 through 1462 Processing helix chain 'A' and resid 1481 through 1497 removed outlier: 3.547A pdb=" N GLU A1496 " --> pdb=" O LYS A1493 " (cutoff:3.500A) Processing helix chain 'A' and resid 1544 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 1576 Processing helix chain 'A' and resid 1622 through 1628 Processing helix chain 'A' and resid 1638 through 1640 No H-bonds generated for 'chain 'A' and resid 1638 through 1640' Processing helix chain 'A' and resid 1645 through 1652 Processing helix chain 'A' and resid 1696 through 1699 No H-bonds generated for 'chain 'A' and resid 1696 through 1699' Processing helix chain 'A' and resid 1710 through 1719 removed outlier: 4.256A pdb=" N CYS A1719 " --> pdb=" O GLU A1715 " (cutoff:3.500A) Processing helix chain 'A' and resid 1726 through 1745 removed outlier: 4.578A pdb=" N LYS A1745 " --> pdb=" O ASP A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1760 through 1772 removed outlier: 3.602A pdb=" N ASN A1771 " --> pdb=" O LEU A1767 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASP A1772 " --> pdb=" O GLN A1768 " (cutoff:3.500A) Processing helix chain 'A' and resid 1784 through 1790 Processing helix chain 'A' and resid 1796 through 1809 Processing helix chain 'A' and resid 1853 through 1867 Proline residue: A1857 - end of helix removed outlier: 4.797A pdb=" N GLU A1860 " --> pdb=" O PRO A1857 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A1862 " --> pdb=" O LEU A1859 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR A1864 " --> pdb=" O SER A1861 " (cutoff:3.500A) Processing helix chain 'A' and resid 1883 through 1893 Processing helix chain 'A' and resid 1908 through 1911 No H-bonds generated for 'chain 'A' and resid 1908 through 1911' Processing helix chain 'A' and resid 1920 through 1941 removed outlier: 3.808A pdb=" N LYS A1941 " --> pdb=" O ASN A1937 " (cutoff:3.500A) Processing helix chain 'A' and resid 1950 through 1957 Processing helix chain 'A' and resid 1968 through 1979 Processing helix chain 'A' and resid 1987 through 2005 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) removed outlier: 4.459A pdb=" N GLU A2005 " --> pdb=" O LYS A2001 " (cutoff:3.500A) Processing helix chain 'A' and resid 2021 through 2024 No H-bonds generated for 'chain 'A' and resid 2021 through 2024' Processing helix chain 'A' and resid 2041 through 2051 removed outlier: 3.804A pdb=" N LEU A2050 " --> pdb=" O ARG A2046 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2097 Processing helix chain 'A' and resid 2110 through 2116 Processing helix chain 'A' and resid 2131 through 2142 removed outlier: 4.055A pdb=" N ILE A2136 " --> pdb=" O LEU A2132 " (cutoff:3.500A) Processing helix chain 'A' and resid 2156 through 2166 Processing helix chain 'A' and resid 2169 through 2177 Processing helix chain 'A' and resid 2199 through 2213 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 2218 through 2228 Processing helix chain 'A' and resid 2239 through 2242 No H-bonds generated for 'chain 'A' and resid 2239 through 2242' Processing helix chain 'A' and resid 2255 through 2279 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 2313 through 2328 removed outlier: 4.177A pdb=" N PHE A2320 " --> pdb=" O LEU A2316 " (cutoff:3.500A) Processing helix chain 'A' and resid 2333 through 2336 No H-bonds generated for 'chain 'A' and resid 2333 through 2336' Processing helix chain 'A' and resid 2342 through 2359 Processing helix chain 'A' and resid 2370 through 2382 Processing helix chain 'A' and resid 2391 through 2406 Proline residue: A2396 - end of helix Processing helix chain 'A' and resid 2760 through 2782 removed outlier: 4.101A pdb=" N LEU A2781 " --> pdb=" O ILE A2777 " (cutoff:3.500A) Processing helix chain 'A' and resid 2789 through 2799 Processing sheet with id= A, first strand: chain 'A' and resid 182 through 184 removed outlier: 6.375A pdb=" N LEU A 224 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 923 through 926 removed outlier: 7.856A pdb=" N LEU A1008 " --> pdb=" O LEU A 967 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1214 through 1218 removed outlier: 6.114A pdb=" N PHE A1312 " --> pdb=" O HIS A1215 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE A1217 " --> pdb=" O PHE A1312 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU A1314 " --> pdb=" O ILE A1217 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 1562 through 1564 removed outlier: 6.399A pdb=" N SER A1701 " --> pdb=" O LEU A1563 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 1587 through 1591 removed outlier: 6.629A pdb=" N TRP A1632 " --> pdb=" O VAL A1588 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A1590 " --> pdb=" O TRP A1632 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU A1634 " --> pdb=" O ILE A1590 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1872 through 1874 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) 598 hydrogen bonds defined for protein. 1659 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: 4.28 Time building geometry restraints manager: 4.54 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: 100.36 - 107.08: 172 107.08 - 113.80: 5916 113.80 - 120.52: 3982 120.52 - 127.23: 4234 127.23 - 133.95: 32 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: 2853 2.78 - 3.31: 10405 3.31 - 3.84: 15482 3.84 - 4.37: 15695 4.37 - 4.90: 24084 Nonbonded interactions: 68519 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 68514 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: 1.690 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: 6.260 Check model and map are aligned: 0.190 Set scattering table: 0.100 Process input model: 33.900 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.240 ------------------------------------------------------------------------------- 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= 0.541 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 : 1.067 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1074 time to fit residues: 8.8646 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.184 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 0.1980 chunk 156 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 83 optimal weight: 0.0980 chunk 161 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 98 optimal weight: 0.0670 chunk 120 optimal weight: 0.9980 chunk 187 optimal weight: 0.9980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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: 0.7811 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.016 10318 Z= 0.087 Angle : 0.474 7.241 14336 Z= 0.264 Chirality : 0.038 0.155 1997 Planarity : 0.002 0.010 2007 Dihedral : 11.112 175.587 2162 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % 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: -3.14 (0.18), residues: 1946 helix: -0.42 (0.15), residues: 1076 sheet: -4.46 (0.39), residues: 92 loop : -4.33 (0.19), residues: 778 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 : 1.231 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1060 time to fit residues: 9.0176 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.188 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 9.9990 chunk 58 optimal weight: 40.0000 chunk 155 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 187 optimal weight: 7.9990 chunk 202 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 185 optimal weight: 20.0000 chunk 63 optimal weight: 0.0060 chunk 150 optimal weight: 9.9990 overall best weight: 3.9800 ------------------------------------------------------------------------------- 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: 0.7938 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10318 Z= 0.197 Angle : 0.537 8.690 14336 Z= 0.318 Chirality : 0.039 0.142 1997 Planarity : 0.002 0.011 2007 Dihedral : 10.497 179.081 2162 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.62 % Favored : 84.38 % 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: -2.42 (0.19), residues: 1946 helix: 0.34 (0.16), residues: 1071 sheet: -4.36 (0.40), residues: 102 loop : -4.21 (0.20), residues: 773 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 : 1.099 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0936 time to fit residues: 8.1152 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 199 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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: 0.7903 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 10318 Z= 0.136 Angle : 0.465 6.919 14336 Z= 0.272 Chirality : 0.039 0.134 1997 Planarity : 0.002 0.009 2007 Dihedral : 10.044 178.586 2162 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.31 % Favored : 86.69 % 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: -1.80 (0.20), residues: 1946 helix: 0.93 (0.16), residues: 1070 sheet: -4.11 (0.43), residues: 102 loop : -4.06 (0.20), residues: 774 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 : 1.179 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0965 time to fit residues: 8.3388 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 178 optimal weight: 0.0060 chunk 50 optimal weight: 20.0000 overall best weight: 2.4004 ------------------------------------------------------------------------------- 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: 0.7897 moved from start: 0.2139 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= 0.125 Angle : 0.445 6.102 14336 Z= 0.260 Chirality : 0.038 0.134 1997 Planarity : 0.002 0.009 2007 Dihedral : 9.723 179.905 2162 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.44 % Favored : 85.56 % 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: -1.38 (0.20), residues: 1946 helix: 1.29 (0.17), residues: 1077 sheet: -4.04 (0.44), residues: 102 loop : -3.95 (0.21), residues: 767 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 : 1.241 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0994 time to fit residues: 8.7178 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 0.0270 chunk 179 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 199 optimal weight: 0.1980 chunk 165 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 104 optimal weight: 0.0060 overall best weight: 1.4458 ------------------------------------------------------------------------------- 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: 0.7856 moved from start: 0.2490 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= 0.085 Angle : 0.402 5.243 14336 Z= 0.233 Chirality : 0.038 0.137 1997 Planarity : 0.001 0.008 2007 Dihedral : 9.244 175.371 2162 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % 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: -0.80 (0.21), residues: 1946 helix: 1.76 (0.17), residues: 1085 sheet: -3.72 (0.48), residues: 98 loop : -3.76 (0.21), residues: 763 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 : 1.252 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0978 time to fit residues: 8.3634 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 3.9990 chunk 22 optimal weight: 30.0000 chunk 113 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 167 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 124 optimal weight: 0.5980 chunk 121 optimal weight: 9.9990 chunk 91 optimal weight: 0.0050 overall best weight: 3.7200 ------------------------------------------------------------------------------- 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: 0.7929 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10318 Z= 0.182 Angle : 0.489 7.106 14336 Z= 0.289 Chirality : 0.039 0.136 1997 Planarity : 0.002 0.010 2007 Dihedral : 9.600 175.094 2162 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.98 % Favored : 84.02 % 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: -1.16 (0.21), residues: 1946 helix: 1.44 (0.17), residues: 1073 sheet: -3.83 (0.49), residues: 93 loop : -3.80 (0.21), residues: 780 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 : 1.222 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1025 time to fit residues: 8.8512 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 7.9990 chunk 79 optimal weight: 0.0170 chunk 118 optimal weight: 0.9980 chunk 59 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 126 optimal weight: 0.7980 chunk 135 optimal weight: 30.0000 chunk 98 optimal weight: 0.0870 chunk 18 optimal weight: 30.0000 chunk 156 optimal weight: 20.0000 overall best weight: 1.7798 ------------------------------------------------------------------------------- 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: 0.7876 moved from start: 0.2581 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= 0.097 Angle : 0.412 5.117 14336 Z= 0.239 Chirality : 0.038 0.133 1997 Planarity : 0.001 0.008 2007 Dihedral : 9.198 172.777 2162 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.18 % Favored : 87.82 % 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: -0.60 (0.21), residues: 1946 helix: 1.92 (0.17), residues: 1076 sheet: -3.72 (0.51), residues: 94 loop : -3.59 (0.21), residues: 776 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 : 1.094 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1020 time to fit residues: 8.7027 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 173 optimal weight: 40.0000 chunk 185 optimal weight: 20.0000 chunk 111 optimal weight: 30.0000 chunk 80 optimal weight: 6.9990 chunk 145 optimal weight: 0.0470 chunk 56 optimal weight: 30.0000 chunk 167 optimal weight: 20.0000 chunk 174 optimal weight: 3.9990 chunk 184 optimal weight: 40.0000 overall best weight: 4.4088 ------------------------------------------------------------------------------- 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: 0.7948 moved from start: 0.2424 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= 0.212 Angle : 0.516 7.687 14336 Z= 0.306 Chirality : 0.039 0.140 1997 Planarity : 0.002 0.010 2007 Dihedral : 9.581 173.392 2162 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.80 % Favored : 83.20 % 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: -1.19 (0.20), residues: 1946 helix: 1.37 (0.16), residues: 1076 sheet: -3.60 (0.55), residues: 85 loop : -3.78 (0.21), 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 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 : 1.855 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0997 time to fit residues: 8.6803 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 10.0000 chunk 195 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 188 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 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: 0.8022 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 : 0.005 0.037 10318 Z= 0.365 Angle : 0.704 11.616 14336 Z= 0.421 Chirality : 0.042 0.167 1997 Planarity : 0.004 0.016 2007 Dihedral : 10.563 179.673 2162 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 20.45 % Favored : 79.50 % 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: -2.66 (0.19), residues: 1946 helix: -0.12 (0.15), residues: 1062 sheet: -3.76 (0.53), residues: 85 loop : -3.96 (0.20), residues: 799 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 : 1.208 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1047 time to fit residues: 8.9593 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.239 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 0.0670 chunk 174 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 150 optimal weight: 8.9990 chunk 24 optimal weight: 30.0000 chunk 45 optimal weight: 20.0000 chunk 163 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 168 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 30 optimal weight: 0.0170 overall best weight: 3.4162 ------------------------------------------------------------------------------- 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 = 0.053139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.046050 restraints weight = 93339.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.046636 restraints weight = 67726.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.047083 restraints weight = 52805.631| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 10318 Z= 0.168 Angle : 0.494 7.490 14336 Z= 0.289 Chirality : 0.039 0.133 1997 Planarity : 0.002 0.009 2007 Dihedral : 9.859 179.287 2162 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.65 % Favored : 85.35 % 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: -1.65 (0.20), residues: 1946 helix: 0.87 (0.16), residues: 1067 sheet: -3.67 (0.54), residues: 86 loop : -3.76 (0.21), residues: 793 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: 1548.85 seconds wall clock time: 28 minutes 45.37 seconds (1725.37 seconds total)