Starting phenix.real_space_refine on Sat Oct 24 19:30:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ygt_72941/10_2026/9ygt_72941.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ygt_72941/10_2026/9ygt_72941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ygt_72941/10_2026/9ygt_72941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ygt_72941/10_2026/9ygt_72941.map" model { file = "/net/cci-nas-00/data/ceres_data/9ygt_72941/10_2026/9ygt_72941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ygt_72941/10_2026/9ygt_72941.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 85 5.16 5 C 8918 2.51 5 N 2395 2.21 5 O 2534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13934 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1774, 13906 Classifications: {'peptide': 1774} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PCIS': 1, 'PTRANS': 76, 'TRANS': 1696} Chain breaks: 11 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 222 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 16, 'GLU:plan': 12, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 131 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.94, per 1000 atoms: 0.21 Number of scatterers: 13934 At special positions: 0 Unit cell: (96.305, 119.68, 161.755, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 2 15.00 O 2534 8.00 N 2395 7.00 C 8918 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 624.2 milliseconds 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3378 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 18 sheets defined 35.7% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 544 through 555 removed outlier: 4.505A pdb=" N ARG A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 Processing helix chain 'A' and resid 585 through 596 Processing helix chain 'A' and resid 599 through 604 removed outlier: 3.695A pdb=" N GLN A 603 " --> pdb=" O ASP A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 612 removed outlier: 3.648A pdb=" N TYR A 612 " --> pdb=" O SER A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 638 removed outlier: 4.298A pdb=" N LYS A 629 " --> pdb=" O HIS A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 657 removed outlier: 4.008A pdb=" N LYS A 647 " --> pdb=" O GLU A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 670 removed outlier: 3.768A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER A 670 " --> pdb=" O LEU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.936A pdb=" N VAL A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N HIS A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 703 removed outlier: 3.596A pdb=" N LYS A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 719 removed outlier: 3.538A pdb=" N GLN A 719 " --> pdb=" O ARG A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 731 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 754 through 764 removed outlier: 3.557A pdb=" N VAL A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 781 Processing helix chain 'A' and resid 786 through 795 Processing helix chain 'A' and resid 814 through 819 removed outlier: 3.790A pdb=" N LEU A 818 " --> pdb=" O GLU A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 850 Processing helix chain 'A' and resid 997 through 1001 Processing helix chain 'A' and resid 1004 through 1013 removed outlier: 3.751A pdb=" N VAL A1008 " --> pdb=" O CYS A1005 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU A1010 " --> pdb=" O SER A1007 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N HIS A1012 " --> pdb=" O HIS A1009 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A1013 " --> pdb=" O LEU A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1053 through 1057 removed outlier: 3.961A pdb=" N MET A1057 " --> pdb=" O LEU A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1104 removed outlier: 4.100A pdb=" N LEU A1102 " --> pdb=" O PRO A1099 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR A1103 " --> pdb=" O GLU A1100 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP A1104 " --> pdb=" O ASN A1101 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1099 through 1104' Processing helix chain 'A' and resid 1189 through 1194 Processing helix chain 'A' and resid 1213 through 1217 Processing helix chain 'A' and resid 1241 through 1245 Processing helix chain 'A' and resid 1261 through 1267 removed outlier: 3.765A pdb=" N ILE A1264 " --> pdb=" O PRO A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1291 removed outlier: 3.570A pdb=" N MET A1288 " --> pdb=" O PRO A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1328 Processing helix chain 'A' and resid 1347 through 1356 Processing helix chain 'A' and resid 1399 through 1403 removed outlier: 4.095A pdb=" N SER A1403 " --> pdb=" O GLU A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1409 removed outlier: 3.514A pdb=" N MET A1409 " --> pdb=" O PRO A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1442 Processing helix chain 'A' and resid 1465 through 1473 removed outlier: 3.980A pdb=" N ILE A1469 " --> pdb=" O CYS A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1509 Processing helix chain 'A' and resid 1517 through 1520 Processing helix chain 'A' and resid 1525 through 1538 Processing helix chain 'A' and resid 1549 through 1560 Processing helix chain 'A' and resid 1568 through 1579 Processing helix chain 'A' and resid 1599 through 1608 removed outlier: 3.541A pdb=" N LEU A1603 " --> pdb=" O GLU A1599 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A1608 " --> pdb=" O CYS A1604 " (cutoff:3.500A) Processing helix chain 'A' and resid 1645 through 1656 removed outlier: 3.597A pdb=" N TYR A1649 " --> pdb=" O TYR A1645 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE A1650 " --> pdb=" O MET A1646 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LYS A1651 " --> pdb=" O SER A1647 " (cutoff:3.500A) Processing helix chain 'A' and resid 1703 through 1714 removed outlier: 4.138A pdb=" N ASN A1710 " --> pdb=" O SER A1706 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A1714 " --> pdb=" O ASN A1710 " (cutoff:3.500A) Processing helix chain 'A' and resid 1770 through 1792 removed outlier: 3.690A pdb=" N LEU A1787 " --> pdb=" O HIS A1783 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A1792 " --> pdb=" O MET A1788 " (cutoff:3.500A) Processing helix chain 'A' and resid 1828 through 1835 Processing helix chain 'A' and resid 1865 through 1869 removed outlier: 3.911A pdb=" N MET A1869 " --> pdb=" O ARG A1866 " (cutoff:3.500A) Processing helix chain 'A' and resid 1871 through 1875 Processing helix chain 'A' and resid 1881 through 1885 removed outlier: 4.326A pdb=" N LEU A1884 " --> pdb=" O PRO A1881 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A1885 " --> pdb=" O GLU A1882 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1881 through 1885' Processing helix chain 'A' and resid 1913 through 1924 removed outlier: 3.955A pdb=" N GLN A1919 " --> pdb=" O ARG A1915 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A1924 " --> pdb=" O GLU A1920 " (cutoff:3.500A) Processing helix chain 'A' and resid 1954 through 1962 removed outlier: 3.559A pdb=" N LEU A1958 " --> pdb=" O SER A1954 " (cutoff:3.500A) Processing helix chain 'A' and resid 1963 through 1966 removed outlier: 3.516A pdb=" N LEU A1966 " --> pdb=" O LYS A1963 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1963 through 1966' Processing helix chain 'A' and resid 1969 through 1988 Processing helix chain 'A' and resid 1996 through 1998 No H-bonds generated for 'chain 'A' and resid 1996 through 1998' Processing helix chain 'A' and resid 2040 through 2046 Processing helix chain 'A' and resid 2051 through 2069 removed outlier: 4.338A pdb=" N ASP A2055 " --> pdb=" O ASN A2051 " (cutoff:3.500A) Processing helix chain 'A' and resid 2071 through 2077 Processing helix chain 'A' and resid 2079 through 2089 removed outlier: 3.975A pdb=" N GLU A2087 " --> pdb=" O PHE A2083 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN A2089 " --> pdb=" O GLU A2085 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2099 Processing helix chain 'A' and resid 2104 through 2115 removed outlier: 3.831A pdb=" N LYS A2109 " --> pdb=" O PRO A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2134 removed outlier: 3.819A pdb=" N SER A2134 " --> pdb=" O ASP A2130 " (cutoff:3.500A) Processing helix chain 'A' and resid 2278 through 2281 removed outlier: 4.216A pdb=" N LYS A2281 " --> pdb=" O LYS A2278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2278 through 2281' Processing helix chain 'A' and resid 2389 through 2397 Processing helix chain 'A' and resid 2499 through 2527 removed outlier: 3.700A pdb=" N GLN A2505 " --> pdb=" O PRO A2501 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 802 through 804 removed outlier: 6.931A pdb=" N LEU A 987 " --> pdb=" O GLU A1017 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1063 through 1064 removed outlier: 7.289A pdb=" N LEU A1063 " --> pdb=" O ASN A1089 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE A1088 " --> pdb=" O ILE A1113 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1177 through 1179 removed outlier: 3.527A pdb=" N ASP A1202 " --> pdb=" O LEU A1178 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU A1201 " --> pdb=" O LEU A1226 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1329 through 1332 removed outlier: 3.643A pdb=" N GLN A1521 " --> pdb=" O TYR A1332 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1373 through 1377 removed outlier: 6.261A pdb=" N LYS A1336 " --> pdb=" O LEU A1414 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1582 through 1583 Processing sheet with id=AA7, first strand: chain 'A' and resid 1690 through 1694 removed outlier: 6.381A pdb=" N TYR A1747 " --> pdb=" O PRO A1768 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER A1743 " --> pdb=" O ALA A1746 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N CYS A1748 " --> pdb=" O ASN A1741 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ASN A1741 " --> pdb=" O CYS A1748 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1840 through 1841 Processing sheet with id=AA9, first strand: chain 'A' and resid 1893 through 1898 removed outlier: 6.634A pdb=" N VAL A1946 " --> pdb=" O LEU A1936 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2000 through 2002 Processing sheet with id=AB2, first strand: chain 'A' and resid 2142 through 2145 removed outlier: 4.373A pdb=" N GLN A2490 " --> pdb=" O ASN A2476 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LYS A2467 " --> pdb=" O LEU A2463 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU A2463 " --> pdb=" O LYS A2467 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A2469 " --> pdb=" O ALA A2461 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYR A2475 " --> pdb=" O VAL A2455 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL A2455 " --> pdb=" O TYR A2475 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2155 through 2157 Processing sheet with id=AB4, first strand: chain 'A' and resid 2199 through 2207 removed outlier: 4.014A pdb=" N GLU A2212 " --> pdb=" O LEU A2207 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A2225 " --> pdb=" O SER A2217 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2245 through 2251 removed outlier: 3.639A pdb=" N CYS A2247 " --> pdb=" O GLY A2266 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A2262 " --> pdb=" O ASN A2251 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2271 through 2273 Processing sheet with id=AB7, first strand: chain 'A' and resid 2300 through 2303 removed outlier: 3.543A pdb=" N MET A2301 " --> pdb=" O GLY A2318 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY A2318 " --> pdb=" O MET A2301 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LEU A2303 " --> pdb=" O TRP A2316 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N TRP A2316 " --> pdb=" O LEU A2303 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2354 through 2359 removed outlier: 6.496A pdb=" N ALA A2366 " --> pdb=" O ILE A2355 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL A2357 " --> pdb=" O TYR A2364 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR A2364 " --> pdb=" O VAL A2357 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A2387 " --> pdb=" O VAL A2373 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A2375 " --> pdb=" O GLY A2385 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY A2385 " --> pdb=" O VAL A2375 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2414 through 2419 removed outlier: 3.789A pdb=" N ARG A2446 " --> pdb=" O LEU A2436 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1284 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: 3.29 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3985 1.33 - 1.46: 2152 1.46 - 1.58: 7931 1.58 - 1.70: 4 1.70 - 1.82: 125 Bond restraints: 14197 Sorted by residual: bond pdb=" C5 GDP A2601 " pdb=" C4 GDP A2601 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C5 GDP A2601 " pdb=" C6 GDP A2601 " ideal model delta sigma weight residual 1.490 1.415 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C6 GDP A2601 " pdb=" N1 GDP A2601 " ideal model delta sigma weight residual 1.337 1.392 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" C LEU A1569 " pdb=" N PRO A1570 " ideal model delta sigma weight residual 1.335 1.373 -0.037 1.36e-02 5.41e+03 7.45e+00 bond pdb=" CB PRO A1083 " pdb=" CG PRO A1083 " ideal model delta sigma weight residual 1.492 1.612 -0.120 5.00e-02 4.00e+02 5.72e+00 ... (remaining 14192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 18718 2.61 - 5.22: 418 5.22 - 7.83: 64 7.83 - 10.44: 17 10.44 - 13.05: 4 Bond angle restraints: 19221 Sorted by residual: angle pdb=" N ILE A1311 " pdb=" CA ILE A1311 " pdb=" C ILE A1311 " ideal model delta sigma weight residual 113.71 109.02 4.69 9.50e-01 1.11e+00 2.44e+01 angle pdb=" CA PRO A1083 " pdb=" N PRO A1083 " pdb=" CD PRO A1083 " ideal model delta sigma weight residual 112.00 105.37 6.63 1.40e+00 5.10e-01 2.24e+01 angle pdb=" C VAL A1541 " pdb=" CA VAL A1541 " pdb=" CB VAL A1541 " ideal model delta sigma weight residual 109.33 113.42 -4.09 9.80e-01 1.04e+00 1.74e+01 angle pdb=" CB LYS A1623 " pdb=" CG LYS A1623 " pdb=" CD LYS A1623 " ideal model delta sigma weight residual 111.30 120.84 -9.54 2.30e+00 1.89e-01 1.72e+01 angle pdb=" N GLN A 650 " pdb=" CA GLN A 650 " pdb=" CB GLN A 650 " ideal model delta sigma weight residual 110.12 116.13 -6.01 1.47e+00 4.63e-01 1.67e+01 ... (remaining 19216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.66: 7837 18.66 - 37.32: 702 37.32 - 55.99: 97 55.99 - 74.65: 24 74.65 - 93.31: 13 Dihedral angle restraints: 8673 sinusoidal: 3490 harmonic: 5183 Sorted by residual: dihedral pdb=" C4' GDP A2601 " pdb=" O5' GDP A2601 " pdb=" C5' GDP A2601 " pdb=" PA GDP A2601 " ideal model delta sinusoidal sigma weight residual 180.02 86.71 93.31 1 2.00e+01 2.50e-03 2.54e+01 dihedral pdb=" CA PHE A1656 " pdb=" C PHE A1656 " pdb=" N GLN A1657 " pdb=" CA GLN A1657 " ideal model delta harmonic sigma weight residual 180.00 155.73 24.27 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA TYR A1992 " pdb=" C TYR A1992 " pdb=" N ARG A1993 " pdb=" CA ARG A1993 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 8670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1677 0.054 - 0.108: 467 0.108 - 0.162: 88 0.162 - 0.216: 12 0.216 - 0.270: 3 Chirality restraints: 2247 Sorted by residual: chirality pdb=" CB ILE A1448 " pdb=" CA ILE A1448 " pdb=" CG1 ILE A1448 " pdb=" CG2 ILE A1448 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB ILE A 835 " pdb=" CA ILE A 835 " pdb=" CG1 ILE A 835 " pdb=" CG2 ILE A 835 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB VAL A1074 " pdb=" CA VAL A1074 " pdb=" CG1 VAL A1074 " pdb=" CG2 VAL A1074 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2244 not shown) Planarity restraints: 2421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A1261 " 0.075 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO A1262 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO A1262 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A1262 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A2381 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" CD GLU A2381 " 0.055 2.00e-02 2.50e+03 pdb=" OE1 GLU A2381 " -0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU A2381 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 754 " 0.048 5.00e-02 4.00e+02 7.32e-02 8.58e+00 pdb=" N PRO A 755 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 755 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 755 " 0.040 5.00e-02 4.00e+02 ... (remaining 2418 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1178 2.74 - 3.28: 14019 3.28 - 3.82: 21993 3.82 - 4.36: 26393 4.36 - 4.90: 44422 Nonbonded interactions: 108005 Sorted by model distance: nonbonded pdb=" O ILE A 835 " pdb=" OG1 THR A 838 " model vdw 2.203 3.040 nonbonded pdb=" O LEU A1195 " pdb=" OG SER A1219 " model vdw 2.206 3.040 nonbonded pdb=" OG1 THR A2223 " pdb=" OG1 THR A2237 " model vdw 2.216 3.040 nonbonded pdb=" OG SER A2166 " pdb=" O LEU A2182 " model vdw 2.227 3.040 nonbonded pdb=" O VAL A2152 " pdb=" OH TYR A2475 " model vdw 2.266 3.040 ... (remaining 108000 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.630 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: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.840 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 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 : 0.005 0.120 14197 Z= 0.219 Angle : 0.961 13.045 19221 Z= 0.496 Chirality : 0.052 0.270 2247 Planarity : 0.007 0.112 2421 Dihedral : 14.435 93.311 5295 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.34 % Favored : 89.43 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.19), residues: 1750 helix: -1.33 (0.20), residues: 573 sheet: -1.47 (0.31), residues: 281 loop : -2.27 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1918 TYR 0.026 0.002 TYR A1992 PHE 0.033 0.002 PHE A1088 TRP 0.048 0.003 TRP A1376 HIS 0.015 0.001 HIS A1998 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.22 (14197) covalent geometry : angle 0.96098 / 0.50 (19221) hydrogen bonds : bond 0.15993 / 11.51 ( 467) hydrogen bonds : angle 7.15716 / 5.18 ( 1284) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 996 ASP cc_start: 0.7883 (t0) cc_final: 0.7679 (t0) REVERT: A 2156 VAL cc_start: 0.8677 (m) cc_final: 0.8427 (t) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.0997 time to fit residues: 31.0348 Evaluate side-chains 165 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.0070 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 720 ASN A 800 ASN A1021 ASN A1437 ASN A1577 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.184514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.145185 restraints weight = 20586.356| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 3.06 r_work: 0.3665 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14197 Z= 0.130 Angle : 0.658 10.689 19221 Z= 0.325 Chirality : 0.045 0.180 2247 Planarity : 0.005 0.060 2421 Dihedral : 5.293 76.898 1893 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.03 % Favored : 90.80 % Rotamer: Outliers : 1.17 % Allowed : 8.03 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.20), residues: 1750 helix: -0.42 (0.22), residues: 568 sheet: -1.39 (0.32), residues: 276 loop : -2.13 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1127 TYR 0.020 0.001 TYR A1992 PHE 0.025 0.002 PHE A1088 TRP 0.017 0.002 TRP A2376 HIS 0.007 0.001 HIS A1998 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (14197) covalent geometry : angle 0.65835 / 0.32 (19221) hydrogen bonds : bond 0.03802 / 2.65 ( 467) hydrogen bonds : angle 5.24050 / 3.84 ( 1284) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.574 Fit side-chains REVERT: A 996 ASP cc_start: 0.7640 (t0) cc_final: 0.7303 (t0) REVERT: A 1407 HIS cc_start: 0.8342 (m90) cc_final: 0.7715 (m90) REVERT: A 1539 LYS cc_start: 0.8101 (ptpp) cc_final: 0.7865 (ptpt) REVERT: A 2315 MET cc_start: 0.3720 (OUTLIER) cc_final: 0.3059 (mtp) REVERT: A 2369 ASN cc_start: 0.5773 (t0) cc_final: 0.5571 (t0) REVERT: A 2376 TRP cc_start: 0.6219 (m100) cc_final: 0.5998 (m100) outliers start: 18 outliers final: 12 residues processed: 186 average time/residue: 0.1022 time to fit residues: 29.4574 Evaluate side-chains 174 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1610 ILE Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1790 GLU Chi-restraints excluded: chain A residue 1791 TRP Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2077 LEU Chi-restraints excluded: chain A residue 2225 LEU Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2315 MET Chi-restraints excluded: chain A residue 2416 THR Chi-restraints excluded: chain A residue 2423 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [67, 53, 32, 139, 0, 66, 24, 122, 110, 152, 150] chunk 67 optimal weight: 0.0670 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.0000 chunk 139 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 0.4980 chunk 24 optimal weight: 0.0170 chunk 122 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 overall best weight: 0.2960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 800 ASN ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.185922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.155480 restraints weight = 20740.723| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.51 r_work: 0.3649 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14197 Z= 0.107 Angle : 0.610 10.507 19221 Z= 0.299 Chirality : 0.043 0.159 2247 Planarity : 0.005 0.057 2421 Dihedral : 4.962 71.527 1893 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.69 % Favored : 91.14 % Rotamer: Outliers : 1.42 % Allowed : 11.07 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.20), residues: 1750 helix: -0.09 (0.22), residues: 569 sheet: -1.49 (0.31), residues: 274 loop : -2.00 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 552 TYR 0.020 0.001 TYR A1992 PHE 0.016 0.001 PHE A1088 TRP 0.012 0.001 TRP A 817 HIS 0.006 0.001 HIS A1998 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (14197) covalent geometry : angle 0.60996 / 0.30 (19221) hydrogen bonds : bond 0.03203 / 2.18 ( 467) hydrogen bonds : angle 4.90050 / 3.58 ( 1284) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.558 Fit side-chains REVERT: A 592 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8535 (p) REVERT: A 650 GLN cc_start: 0.8514 (mp10) cc_final: 0.8292 (mp10) REVERT: A 693 ASN cc_start: 0.7690 (m110) cc_final: 0.7327 (m110) REVERT: A 996 ASP cc_start: 0.7708 (t0) cc_final: 0.7315 (t0) REVERT: A 1407 HIS cc_start: 0.8348 (m90) cc_final: 0.8137 (m90) REVERT: A 1764 LYS cc_start: 0.7824 (ttpt) cc_final: 0.7493 (ttpt) REVERT: A 2315 MET cc_start: 0.3974 (OUTLIER) cc_final: 0.3408 (mtp) REVERT: A 2369 ASN cc_start: 0.5704 (t0) cc_final: 0.5441 (t0) REVERT: A 2376 TRP cc_start: 0.6272 (m100) cc_final: 0.5832 (m-90) outliers start: 22 outliers final: 12 residues processed: 190 average time/residue: 0.0957 time to fit residues: 28.9809 Evaluate side-chains 178 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 800 ASN Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1610 ILE Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1790 GLU Chi-restraints excluded: chain A residue 1791 TRP Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2077 LEU Chi-restraints excluded: chain A residue 2293 ILE Chi-restraints excluded: chain A residue 2315 MET Chi-restraints excluded: chain A residue 2416 THR Chi-restraints excluded: chain A residue 2423 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [21, 93, 39, 164, 84, 152, 28, 115, 67, 170, 53] chunk 21 optimal weight: 0.6980 chunk 93 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 164 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 67 optimal weight: 0.0000 chunk 170 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2220 GLN ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.183900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.143089 restraints weight = 20706.395| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.85 r_work: 0.3654 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14197 Z= 0.118 Angle : 0.611 10.331 19221 Z= 0.298 Chirality : 0.044 0.172 2247 Planarity : 0.004 0.057 2421 Dihedral : 4.859 67.408 1893 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.03 % Favored : 90.80 % Rotamer: Outliers : 1.94 % Allowed : 13.27 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.20), residues: 1750 helix: 0.04 (0.23), residues: 568 sheet: -1.43 (0.32), residues: 279 loop : -1.99 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 552 TYR 0.017 0.001 TYR A1992 PHE 0.020 0.001 PHE A1088 TRP 0.012 0.002 TRP A 817 HIS 0.005 0.001 HIS A1998 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (14197) covalent geometry : angle 0.61111 / 0.30 (19221) hydrogen bonds : bond 0.03052 / 2.09 ( 467) hydrogen bonds : angle 4.80179 / 3.51 ( 1284) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 592 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8665 (p) REVERT: A 996 ASP cc_start: 0.7692 (t0) cc_final: 0.7316 (t0) REVERT: A 2315 MET cc_start: 0.3795 (OUTLIER) cc_final: 0.3283 (mtp) REVERT: A 2316 TRP cc_start: 0.7008 (m100) cc_final: 0.6197 (m100) REVERT: A 2364 TYR cc_start: 0.7416 (m-80) cc_final: 0.7215 (m-80) REVERT: A 2369 ASN cc_start: 0.5860 (t0) cc_final: 0.5613 (t0) REVERT: A 2376 TRP cc_start: 0.6371 (m100) cc_final: 0.6091 (m-90) outliers start: 30 outliers final: 18 residues processed: 194 average time/residue: 0.0946 time to fit residues: 29.4117 Evaluate side-chains 178 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1774 CYS Chi-restraints excluded: chain A residue 1790 GLU Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2077 LEU Chi-restraints excluded: chain A residue 2293 ILE Chi-restraints excluded: chain A residue 2315 MET Chi-restraints excluded: chain A residue 2416 THR Chi-restraints excluded: chain A residue 2423 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [51, 144, 165, 94, 26, 112, 39, 80, 49, 82, 95] chunk 51 optimal weight: 0.6980 chunk 144 optimal weight: 0.0980 chunk 165 optimal weight: 0.0970 chunk 94 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 112 optimal weight: 0.0170 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 49 optimal weight: 0.3980 chunk 82 optimal weight: 0.2980 chunk 95 optimal weight: 0.9980 overall best weight: 0.1816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1779 GLN A2051 ASN A2510 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.186448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.156820 restraints weight = 20744.646| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.47 r_work: 0.3667 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14197 Z= 0.098 Angle : 0.593 11.197 19221 Z= 0.287 Chirality : 0.043 0.173 2247 Planarity : 0.004 0.057 2421 Dihedral : 4.653 62.982 1893 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.00 % Favored : 91.83 % Rotamer: Outliers : 1.68 % Allowed : 14.95 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.20), residues: 1750 helix: 0.15 (0.23), residues: 569 sheet: -1.43 (0.32), residues: 270 loop : -1.90 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 552 TYR 0.017 0.001 TYR A1992 PHE 0.013 0.001 PHE A1321 TRP 0.015 0.001 TRP A2376 HIS 0.005 0.000 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (14197) covalent geometry : angle 0.59302 / 0.29 (19221) hydrogen bonds : bond 0.02799 / 1.90 ( 467) hydrogen bonds : angle 4.65740 / 3.41 ( 1284) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 592 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8591 (p) REVERT: A 693 ASN cc_start: 0.7705 (m110) cc_final: 0.7347 (m110) REVERT: A 996 ASP cc_start: 0.7800 (t0) cc_final: 0.7496 (t0) REVERT: A 1064 ASP cc_start: 0.8229 (t0) cc_final: 0.7754 (t0) REVERT: A 1407 HIS cc_start: 0.8330 (m90) cc_final: 0.8052 (m90) REVERT: A 2305 GLU cc_start: 0.7392 (tt0) cc_final: 0.6967 (tt0) REVERT: A 2315 MET cc_start: 0.4131 (OUTLIER) cc_final: 0.3540 (mtp) REVERT: A 2376 TRP cc_start: 0.6590 (m100) cc_final: 0.6336 (m-90) outliers start: 26 outliers final: 17 residues processed: 188 average time/residue: 0.0953 time to fit residues: 28.4570 Evaluate side-chains 178 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1610 ILE Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2077 LEU Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2293 ILE Chi-restraints excluded: chain A residue 2315 MET Chi-restraints excluded: chain A residue 2416 THR Chi-restraints excluded: chain A residue 2423 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [87, 16, 146, 6, 41, 20, 108, 142, 137, 175, 18] chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 108 optimal weight: 0.3980 chunk 142 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1182 GLN A1342 ASN A2053 GLN ** A2490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.180427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.139721 restraints weight = 20559.467| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 3.03 r_work: 0.3599 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14197 Z= 0.165 Angle : 0.659 10.857 19221 Z= 0.321 Chirality : 0.045 0.201 2247 Planarity : 0.005 0.058 2421 Dihedral : 4.925 62.318 1893 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.43 % Favored : 90.40 % Rotamer: Outliers : 2.52 % Allowed : 14.30 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.20), residues: 1750 helix: 0.22 (0.23), residues: 561 sheet: -1.40 (0.32), residues: 283 loop : -1.98 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 552 TYR 0.016 0.002 TYR A2249 PHE 0.025 0.002 PHE A1088 TRP 0.017 0.002 TRP A1393 HIS 0.004 0.001 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.16 (14197) covalent geometry : angle 0.65865 / 0.32 (19221) hydrogen bonds : bond 0.03152 / 2.17 ( 467) hydrogen bonds : angle 4.75173 / 3.44 ( 1284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 592 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8739 (p) REVERT: A 996 ASP cc_start: 0.7752 (t0) cc_final: 0.7427 (t0) REVERT: A 2305 GLU cc_start: 0.7408 (tt0) cc_final: 0.6946 (tt0) REVERT: A 2315 MET cc_start: 0.3835 (OUTLIER) cc_final: 0.3414 (mtp) REVERT: A 2316 TRP cc_start: 0.6961 (m100) cc_final: 0.6609 (m100) REVERT: A 2376 TRP cc_start: 0.6531 (m100) cc_final: 0.6297 (m-90) REVERT: A 2435 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6969 (mt) outliers start: 39 outliers final: 24 residues processed: 192 average time/residue: 0.0991 time to fit residues: 29.9370 Evaluate side-chains 188 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1790 GLU Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2077 LEU Chi-restraints excluded: chain A residue 2264 LEU Chi-restraints excluded: chain A residue 2293 ILE Chi-restraints excluded: chain A residue 2315 MET Chi-restraints excluded: chain A residue 2416 THR Chi-restraints excluded: chain A residue 2423 THR Chi-restraints excluded: chain A residue 2434 ILE Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2441 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [60, 44, 152, 173, 30, 11, 145, 74, 108, 118, 35] chunk 60 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 152 optimal weight: 0.0970 chunk 173 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 GLN ** A1407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1879 GLN ** A2490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.189216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.159959 restraints weight = 20403.104| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.60 r_work: 0.3706 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14197 Z= 0.120 Angle : 0.638 15.543 19221 Z= 0.306 Chirality : 0.044 0.225 2247 Planarity : 0.004 0.057 2421 Dihedral : 4.811 59.611 1893 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.97 % Favored : 90.86 % Rotamer: Outliers : 2.46 % Allowed : 14.76 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.20), residues: 1750 helix: 0.24 (0.23), residues: 567 sheet: -1.56 (0.32), residues: 271 loop : -1.96 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1895 TYR 0.016 0.001 TYR A1992 PHE 0.016 0.001 PHE A1088 TRP 0.015 0.002 TRP A1742 HIS 0.003 0.001 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (14197) covalent geometry : angle 0.63756 / 0.31 (19221) hydrogen bonds : bond 0.02906 / 2.00 ( 467) hydrogen bonds : angle 4.63781 / 3.37 ( 1284) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 996 ASP cc_start: 0.7880 (t0) cc_final: 0.7504 (t0) REVERT: A 2289 LYS cc_start: 0.6581 (pttm) cc_final: 0.4941 (ttpt) REVERT: A 2305 GLU cc_start: 0.7476 (tt0) cc_final: 0.7099 (tt0) REVERT: A 2315 MET cc_start: 0.4350 (OUTLIER) cc_final: 0.3857 (mtp) REVERT: A 2316 TRP cc_start: 0.7407 (m100) cc_final: 0.7054 (m100) REVERT: A 2435 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7177 (mt) outliers start: 38 outliers final: 26 residues processed: 187 average time/residue: 0.0929 time to fit residues: 27.7084 Evaluate side-chains 183 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1607 MET Chi-restraints excluded: chain A residue 1610 ILE Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1826 LEU Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2077 LEU Chi-restraints excluded: chain A residue 2293 ILE Chi-restraints excluded: chain A residue 2315 MET Chi-restraints excluded: chain A residue 2383 LEU Chi-restraints excluded: chain A residue 2416 THR Chi-restraints excluded: chain A residue 2423 THR Chi-restraints excluded: chain A residue 2434 ILE Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2441 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [105, 9, 140, 117, 99, 74, 52, 37, 155, 60, 130] chunk 105 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.187180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.159205 restraints weight = 20240.702| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 2.37 r_work: 0.3682 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14197 Z= 0.147 Angle : 0.668 11.497 19221 Z= 0.323 Chirality : 0.045 0.207 2247 Planarity : 0.005 0.066 2421 Dihedral : 4.909 59.372 1893 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.77 % Favored : 90.06 % Rotamer: Outliers : 2.39 % Allowed : 14.76 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.20), residues: 1750 helix: 0.24 (0.23), residues: 568 sheet: -1.44 (0.32), residues: 280 loop : -2.06 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1895 TYR 0.014 0.001 TYR A1992 PHE 0.019 0.001 PHE A1088 TRP 0.026 0.002 TRP A2168 HIS 0.004 0.001 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (14197) covalent geometry : angle 0.66756 / 0.32 (19221) hydrogen bonds : bond 0.03089 / 2.13 ( 467) hydrogen bonds : angle 4.65716 / 3.38 ( 1284) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 996 ASP cc_start: 0.7969 (t0) cc_final: 0.7538 (t0) REVERT: A 2289 LYS cc_start: 0.6789 (pttm) cc_final: 0.5116 (ttpt) REVERT: A 2305 GLU cc_start: 0.7547 (tt0) cc_final: 0.7183 (tt0) REVERT: A 2315 MET cc_start: 0.4363 (OUTLIER) cc_final: 0.3874 (mtp) REVERT: A 2316 TRP cc_start: 0.7371 (m100) cc_final: 0.7094 (m100) REVERT: A 2435 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7199 (mt) outliers start: 37 outliers final: 26 residues processed: 187 average time/residue: 0.0962 time to fit residues: 28.7262 Evaluate side-chains 190 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1607 MET Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2077 LEU Chi-restraints excluded: chain A residue 2293 ILE Chi-restraints excluded: chain A residue 2315 MET Chi-restraints excluded: chain A residue 2383 LEU Chi-restraints excluded: chain A residue 2416 THR Chi-restraints excluded: chain A residue 2423 THR Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2434 ILE Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2441 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [123, 78, 120, 18, 116, 56, 11, 175, 74, 150, 90] chunk 123 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 116 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1879 GLN ** A2490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.187696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.158237 restraints weight = 20411.086| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 2.59 r_work: 0.3661 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14197 Z= 0.135 Angle : 0.674 16.772 19221 Z= 0.324 Chirality : 0.045 0.227 2247 Planarity : 0.005 0.062 2421 Dihedral : 4.878 58.363 1893 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.83 % Favored : 90.00 % Rotamer: Outliers : 2.14 % Allowed : 15.40 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.20), residues: 1750 helix: 0.28 (0.23), residues: 567 sheet: -1.65 (0.32), residues: 259 loop : -2.03 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1895 TYR 0.014 0.001 TYR A1992 PHE 0.017 0.001 PHE A1088 TRP 0.027 0.002 TRP A2168 HIS 0.003 0.001 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (14197) covalent geometry : angle 0.67438 / 0.32 (19221) hydrogen bonds : bond 0.03045 / 2.09 ( 467) hydrogen bonds : angle 4.60905 / 3.34 ( 1284) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 684 MET cc_start: 0.6169 (mtp) cc_final: 0.5566 (pmm) REVERT: A 996 ASP cc_start: 0.7908 (t0) cc_final: 0.7520 (t0) REVERT: A 1607 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6718 (ttm) REVERT: A 1869 MET cc_start: 0.7692 (mmm) cc_final: 0.7385 (mmt) REVERT: A 1961 GLN cc_start: 0.8017 (pp30) cc_final: 0.7272 (tt0) REVERT: A 1962 ASP cc_start: 0.7401 (t0) cc_final: 0.7003 (m-30) REVERT: A 2289 LYS cc_start: 0.6799 (pttm) cc_final: 0.5587 (pttt) REVERT: A 2305 GLU cc_start: 0.7535 (tt0) cc_final: 0.7195 (tt0) REVERT: A 2315 MET cc_start: 0.4268 (OUTLIER) cc_final: 0.3781 (mtp) REVERT: A 2316 TRP cc_start: 0.7412 (m100) cc_final: 0.7110 (m100) REVERT: A 2435 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7214 (mt) outliers start: 33 outliers final: 26 residues processed: 177 average time/residue: 0.0919 time to fit residues: 26.2994 Evaluate side-chains 182 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1607 MET Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2077 LEU Chi-restraints excluded: chain A residue 2293 ILE Chi-restraints excluded: chain A residue 2315 MET Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2383 LEU Chi-restraints excluded: chain A residue 2416 THR Chi-restraints excluded: chain A residue 2423 THR Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2434 ILE Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2441 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [33, 24, 130, 42, 116, 122, 151, 120, 114, 55, 173] chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 42 optimal weight: 0.0070 chunk 116 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 151 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 114 optimal weight: 0.0170 chunk 55 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1407 HIS ** A1486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.189285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.160957 restraints weight = 20317.533| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.56 r_work: 0.3706 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14197 Z= 0.118 Angle : 0.661 16.345 19221 Z= 0.315 Chirality : 0.044 0.234 2247 Planarity : 0.005 0.069 2421 Dihedral : 4.745 56.398 1893 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.60 % Favored : 90.23 % Rotamer: Outliers : 1.81 % Allowed : 15.79 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.20), residues: 1750 helix: 0.43 (0.23), residues: 562 sheet: -1.63 (0.32), residues: 252 loop : -1.94 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1895 TYR 0.015 0.001 TYR A1992 PHE 0.014 0.001 PHE A1321 TRP 0.019 0.002 TRP A2168 HIS 0.003 0.001 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (14197) covalent geometry : angle 0.66084 / 0.32 (19221) hydrogen bonds : bond 0.02922 / 2.01 ( 467) hydrogen bonds : angle 4.52866 / 3.28 ( 1284) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 684 MET cc_start: 0.6122 (mtp) cc_final: 0.5582 (pmm) REVERT: A 996 ASP cc_start: 0.7879 (t0) cc_final: 0.7485 (t0) REVERT: A 1335 MET cc_start: 0.8061 (ttm) cc_final: 0.7853 (ttm) REVERT: A 1355 MET cc_start: 0.6727 (mmp) cc_final: 0.6364 (mmp) REVERT: A 1457 SER cc_start: 0.7206 (t) cc_final: 0.6626 (m) REVERT: A 1607 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6647 (ttm) REVERT: A 1656 PHE cc_start: 0.5061 (m-10) cc_final: 0.4821 (m-10) REVERT: A 2289 LYS cc_start: 0.6699 (pttm) cc_final: 0.5081 (ttpt) REVERT: A 2305 GLU cc_start: 0.7513 (tt0) cc_final: 0.7168 (tt0) REVERT: A 2315 MET cc_start: 0.4408 (OUTLIER) cc_final: 0.3972 (mtp) REVERT: A 2316 TRP cc_start: 0.7378 (m100) cc_final: 0.7085 (m100) outliers start: 28 outliers final: 24 residues processed: 174 average time/residue: 0.0928 time to fit residues: 25.9527 Evaluate side-chains 181 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1607 MET Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2077 LEU Chi-restraints excluded: chain A residue 2293 ILE Chi-restraints excluded: chain A residue 2315 MET Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2383 LEU Chi-restraints excluded: chain A residue 2416 THR Chi-restraints excluded: chain A residue 2423 THR Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2441 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [38, 105, 159, 98, 143, 122, 117, 49, 4, 31, 63] chunk 38 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 98 optimal weight: 0.2980 chunk 143 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 49 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 693 ASN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1879 GLN ** A2490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.188993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.160632 restraints weight = 20335.722| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 2.55 r_work: 0.3706 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14197 Z= 0.121 Angle : 0.673 16.801 19221 Z= 0.320 Chirality : 0.044 0.228 2247 Planarity : 0.005 0.067 2421 Dihedral : 4.738 56.242 1893 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.66 % Favored : 90.17 % Rotamer: Outliers : 2.07 % Allowed : 15.73 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.20), residues: 1750 helix: 0.45 (0.23), residues: 563 sheet: -1.62 (0.32), residues: 262 loop : -1.91 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1895 TYR 0.017 0.001 TYR A1419 PHE 0.015 0.001 PHE A1883 TRP 0.018 0.002 TRP A2168 HIS 0.003 0.001 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (14197) covalent geometry : angle 0.67283 / 0.32 (19221) hydrogen bonds : bond 0.02888 / 1.98 ( 467) hydrogen bonds : angle 4.54217 / 3.29 ( 1284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3184.92 seconds wall clock time: 55 minutes 25.75 seconds (3325.75 seconds total)