Starting phenix.real_space_refine (version: 1.20rc4) on Thu Dec 2 00:50:06 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6or5_9032/12_2021/6or5_9032_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6or5_9032/12_2021/6or5_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_2021/6or5_9032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6or5_9032/12_2021/6or5_9032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6or5_9032/12_2021/6or5_9032_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6or5_9032/12_2021/6or5_9032_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/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: {'undetermined': 5, 'peptide': 2058} 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: 6.75, per 1000 atoms: 0.65 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 Amimo 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: 4.85 Conformation dependent library (CDL) restraints added in 2.3 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: 4.09 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: 4.58 Time building geometry restraints manager: 5.20 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=" O3G ANP A7204 " pdb=" PG ANP A7204 " ideal model delta sigma weight residual 1.582 1.487 0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" O3G ANP A7205 " pdb=" PG ANP A7205 " ideal model delta sigma weight residual 1.582 1.490 0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" O3G ANP A7201 " pdb=" PG ANP A7201 " ideal model delta sigma weight residual 1.582 1.490 0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" O3G ANP A7203 " pdb=" PG ANP A7203 " ideal model delta sigma weight residual 1.582 1.491 0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" O1G ANP A7203 " pdb=" PG ANP A7203 " ideal model delta sigma weight residual 1.496 1.581 -0.085 2.00e-02 2.50e+03 1.82e+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=" 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=" N VAL A2786 " pdb=" CA VAL A2786 " pdb=" C VAL A2786 " ideal model delta sigma weight residual 106.21 111.81 -5.60 1.07e+00 8.73e-01 2.74e+01 angle pdb=" N LEU A 48 " pdb=" CA LEU A 48 " pdb=" C LEU A 48 " ideal model delta sigma weight residual 113.17 119.21 -6.04 1.26e+00 6.30e-01 2.30e+01 angle pdb=" C ASN A1407 " pdb=" N LYS A1408 " pdb=" CA LYS A1408 " ideal model delta sigma weight residual 121.54 130.12 -8.58 1.91e+00 2.74e-01 2.02e+01 angle pdb=" C GLU A1005 " pdb=" N PHE A1006 " pdb=" CA PHE A1006 " ideal model delta sigma weight residual 121.54 130.10 -8.56 1.91e+00 2.74e-01 2.01e+01 ... (remaining 14331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 5983 35.75 - 71.49: 17 71.49 - 107.24: 2 107.24 - 142.99: 3 142.99 - 178.73: 1 Dihedral angle restraints: 6006 sinusoidal: 50 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 6003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1716 0.069 - 0.137: 266 0.137 - 0.206: 17 0.206 - 0.274: 5 0.274 - 0.343: 3 Chirality restraints: 2007 Sorted by residual: chirality pdb=" PB ANP A7201 " pdb=" N3B ANP A7201 " pdb=" O2B ANP A7201 " pdb=" O3A ANP A7201 " both_signs ideal model delta sigma weight residual True 3.13 2.79 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" PA ANP A7203 " pdb=" O2A ANP A7203 " pdb=" O3A ANP A7203 " pdb=" O5' ANP A7203 " both_signs ideal model delta sigma weight residual True 3.18 2.88 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" PA ANP A7204 " pdb=" O2A ANP A7204 " pdb=" O3A ANP A7204 " pdb=" O5' ANP A7204 " both_signs ideal model delta sigma weight residual True 3.18 2.91 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 2004 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 2.440 nonbonded pdb=" O1B ANP A7201 " pdb=" O2A ANP A7201 " model vdw 2.261 2.440 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 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. 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 Write .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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.430 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.090 Process input model: 33.070 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.370 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 44.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 : 0.006 0.095 10318 Z= 0.445 Angle : 0.933 11.733 14336 Z= 0.591 Chirality : 0.050 0.343 2007 Planarity : 0.005 0.037 2007 Dihedral : 11.504 178.734 2052 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 % 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 *********************** 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 : 1.215 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0967 time to fit residues: 8.3207 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.289 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6624 ------------------------------------------------------------------------------- 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: 8.9990 chunk 86 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 161 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 187 optimal weight: 0.9980 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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: 0.7836 moved from start: 0.1143 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= 0.119 Angle : 0.493 6.798 14336 Z= 0.294 Chirality : 0.039 0.137 2007 Planarity : 0.002 0.012 2007 Dihedral : 9.960 179.866 2052 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.54 % Favored : 87.46 % Rotamer Outliers : 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: -3.44 (0.18), residues: 1946 helix: -0.68 (0.15), residues: 1065 sheet: -4.55 (0.37), residues: 102 loop : -4.37 (0.19), residues: 779 *********************** 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 : 1.209 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0920 time to fit residues: 7.8218 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4420 ------------------------------------------------------------------------------- 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: 10.0000 chunk 58 optimal weight: 20.0000 chunk 155 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 187 optimal weight: 6.9990 chunk 202 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 chunk 185 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 overall best weight: 4.6986 ------------------------------------------------------------------------------- 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: 0.7912 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 10318 Z= 0.231 Angle : 0.587 8.471 14336 Z= 0.352 Chirality : 0.040 0.191 2007 Planarity : 0.003 0.013 2007 Dihedral : 9.895 179.219 2052 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 18.14 % Favored : 81.81 % Rotamer Outliers : 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: -2.94 (0.19), residues: 1946 helix: -0.17 (0.15), residues: 1065 sheet: -4.38 (0.40), residues: 102 loop : -4.30 (0.20), residues: 779 *********************** 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 : 1.320 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0947 time to fit residues: 8.2979 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.296 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7003 ------------------------------------------------------------------------------- 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: 20.0000 chunk 140 optimal weight: 0.0170 chunk 97 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 125 optimal weight: 5.9990 chunk 188 optimal weight: 0.0070 chunk 199 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 178 optimal weight: 0.9980 chunk 53 optimal weight: 0.0970 overall best weight: 1.4236 ------------------------------------------------------------------------------- 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: 0.7819 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.012 10318 Z= 0.092 Angle : 0.435 5.245 14336 Z= 0.257 Chirality : 0.038 0.137 2007 Planarity : 0.002 0.009 2007 Dihedral : 9.255 178.280 2052 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer Outliers : 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: -1.74 (0.20), residues: 1946 helix: 0.97 (0.16), residues: 1069 sheet: -4.12 (0.43), residues: 102 loop : -4.01 (0.21), residues: 775 *********************** 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 : 1.135 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1003 time to fit residues: 8.6331 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.284 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6019 ------------------------------------------------------------------------------- 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: 3.9990 chunk 113 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 chunk 169 optimal weight: 0.0670 chunk 137 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 178 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 overall best weight: 3.5924 ------------------------------------------------------------------------------- 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: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 10318 Z= 0.177 Angle : 0.496 6.572 14336 Z= 0.296 Chirality : 0.039 0.155 2007 Planarity : 0.002 0.010 2007 Dihedral : 9.265 178.551 2052 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.60 % Favored : 83.40 % Rotamer Outliers : 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: -1.78 (0.20), residues: 1946 helix: 0.98 (0.16), residues: 1064 sheet: -4.00 (0.43), residues: 107 loop : -4.10 (0.20), residues: 775 *********************** 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 : 1.205 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0984 time to fit residues: 8.3512 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.194 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6506 ------------------------------------------------------------------------------- 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: 9.9990 chunk 179 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 116 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 199 optimal weight: 0.4980 chunk 165 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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: 0.7829 moved from start: 0.2029 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= 0.105 Angle : 0.427 4.815 14336 Z= 0.252 Chirality : 0.038 0.136 2007 Planarity : 0.001 0.009 2007 Dihedral : 9.028 178.195 2052 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer Outliers : 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: -1.20 (0.21), residues: 1946 helix: 1.48 (0.17), residues: 1071 sheet: -3.85 (0.47), residues: 99 loop : -3.92 (0.21), residues: 776 *********************** 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 : 1.220 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1007 time to fit residues: 8.7262 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5179 ------------------------------------------------------------------------------- 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: 0.0670 chunk 22 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 145 optimal weight: 0.5980 chunk 112 optimal weight: 8.9990 chunk 167 optimal weight: 20.0000 chunk 111 optimal weight: 0.8980 chunk 198 optimal weight: 10.0000 chunk 124 optimal weight: 0.0070 chunk 121 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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: 0.7757 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.012 10318 Z= 0.066 Angle : 0.382 4.675 14336 Z= 0.222 Chirality : 0.038 0.143 2007 Planarity : 0.001 0.008 2007 Dihedral : 8.579 178.043 2052 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer Outliers : 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: -0.44 (0.21), residues: 1946 helix: 2.03 (0.17), residues: 1095 sheet: -3.60 (0.51), residues: 86 loop : -3.64 (0.22), residues: 765 *********************** 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 : 0.904 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1067 time to fit residues: 9.3068 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5142 ------------------------------------------------------------------------------- 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: 0.0470 chunk 79 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 59 optimal weight: 0.0570 chunk 39 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 135 optimal weight: 30.0000 chunk 98 optimal weight: 0.9990 chunk 18 optimal weight: 20.0000 chunk 156 optimal weight: 30.0000 overall best weight: 2.4202 ------------------------------------------------------------------------------- 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: 0.7818 moved from start: 0.2404 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= 0.125 Angle : 0.422 4.891 14336 Z= 0.250 Chirality : 0.039 0.136 2007 Planarity : 0.002 0.009 2007 Dihedral : 8.616 178.742 2052 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % Rotamer Outliers : 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: -0.50 (0.21), residues: 1946 helix: 1.98 (0.17), residues: 1086 sheet: -3.56 (0.49), residues: 99 loop : -3.60 (0.22), residues: 761 *********************** 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 : 1.268 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0996 time to fit residues: 8.6476 Evaluate side-chains 36 residues out of total 1855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.315 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6809 ------------------------------------------------------------------------------- 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: 0.7980 chunk 173 optimal weight: 0.0010 chunk 185 optimal weight: 7.9990 chunk 111 optimal weight: 0.0370 chunk 80 optimal weight: 0.5980 chunk 145 optimal weight: 8.9990 chunk 56 optimal weight: 30.0000 chunk 167 optimal weight: 0.5980 chunk 174 optimal weight: 20.0000 chunk 184 optimal weight: 20.0000 overall best weight: 0.4064 ------------------------------------------------------------------------------- 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: 0.7745 moved from start: 0.2768 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= 0.063 Angle : 0.374 4.624 14336 Z= 0.217 Chirality : 0.038 0.142 2007 Planarity : 0.001 0.007 2007 Dihedral : 8.388 177.881 2052 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer Outliers : 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: -0.12 (0.22), residues: 1946 helix: 2.30 (0.17), residues: 1092 sheet: -3.35 (0.50), residues: 97 loop : -3.51 (0.22), residues: 757 *********************** 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 : 1.277 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0966 time to fit residues: 8.2843 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5583 ------------------------------------------------------------------------------- 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: 10.0000 chunk 92 optimal weight: 0.0000 chunk 136 optimal weight: 0.8980 chunk 205 optimal weight: 10.0000 chunk 188 optimal weight: 0.0070 chunk 163 optimal weight: 0.0070 chunk 16 optimal weight: 2.9990 chunk 126 optimal weight: 0.3980 chunk 100 optimal weight: 8.9990 overall best weight: 0.2620 ------------------------------------------------------------------------------- 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: 0.7711 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.009 10318 Z= 0.058 Angle : 0.355 4.619 14336 Z= 0.207 Chirality : 0.038 0.144 2007 Planarity : 0.001 0.007 2007 Dihedral : 8.024 177.930 2052 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer Outliers : 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: 0.11 (0.22), residues: 1946 helix: 2.41 (0.17), residues: 1116 sheet: -3.09 (0.51), residues: 97 loop : -3.49 (0.22), residues: 733 ********************** 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 : 1.221 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1026 time to fit residues: 8.7354 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5981 ------------------------------------------------------------------------------- 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: 2.9990 chunk 174 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 150 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 163 optimal weight: 0.4980 chunk 68 optimal weight: 20.0000 chunk 168 optimal weight: 0.0980 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 = 0.3288 r_free = 0.3288 target = 0.055229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.047874 restraints weight = 92316.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.048509 restraints weight = 67085.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.048983 restraints weight = 52316.661| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2926 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= 0.096 Angle : 0.385 4.573 14336 Z= 0.227 Chirality : 0.038 0.138 2007 Planarity : 0.001 0.008 2007 Dihedral : 8.137 178.711 2052 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer Outliers : 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: 0.12 (0.22), residues: 1946 helix: 2.43 (0.17), residues: 1101 sheet: -3.14 (0.50), residues: 97 loop : -3.37 (0.22), residues: 748 =============================================================================== Job complete usr+sys time: 1414.32 seconds wall clock time: 28 minutes 5.06 seconds (1685.06 seconds total)