Starting phenix.real_space_refine on Wed Feb 4 12:36:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hma_52290/02_2026/9hma_52290.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hma_52290/02_2026/9hma_52290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hma_52290/02_2026/9hma_52290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hma_52290/02_2026/9hma_52290.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hma_52290/02_2026/9hma_52290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hma_52290/02_2026/9hma_52290.map" } resolution = 3.3 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= -0.017 sd= 0.319 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 Zn 1 6.06 5 S 47 5.16 5 C 6539 2.51 5 N 1820 2.21 5 O 1926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10333 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1400, 10332 Classifications: {'peptide': 1400} Incomplete info: {'backbone_only': 12, 'truncation_to_alanine': 154} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1332} Chain breaks: 7 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 623 Unresolved non-hydrogen angles: 806 Unresolved non-hydrogen dihedrals: 518 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'ARG:plan': 8, 'TYR:plan': 11, 'GLU:plan': 10, 'GLN:plan1': 17, 'PHE:plan': 10, 'ASP:plan': 8, 'HIS:plan': 5, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 347 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5155 SG CYS A1203 18.219 72.058 96.862 1.00 30.00 S ATOM 5169 SG CYS A1205 21.984 71.453 97.498 1.00 30.00 S ATOM 5189 SG CYS A1208 19.391 69.091 99.045 1.00 30.00 S Time building chain proxies: 2.28, per 1000 atoms: 0.22 Number of scatterers: 10333 At special positions: 0 Unit cell: (87.831, 90.7587, 170.783, 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) Zn 1 29.99 S 47 16.00 O 1926 8.00 N 1820 7.00 C 6539 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 694 " - pdb=" SG CYS A 744 " distance=2.04 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: 0.85 Conformation dependent library (CDL) restraints added in 433.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" ND1 HIS A1199 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1205 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1208 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1203 " Number of angles added : 3 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2624 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 2 sheets defined 73.5% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 329 through 350 Processing helix chain 'A' and resid 357 through 381 removed outlier: 4.100A pdb=" N LEU A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 414 Processing helix chain 'A' and resid 418 through 442 removed outlier: 3.634A pdb=" N ASP A 422 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 470 Processing helix chain 'A' and resid 472 through 547 Proline residue: A 539 - end of helix removed outlier: 3.579A pdb=" N HIS A 543 " --> pdb=" O PRO A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 575 Processing helix chain 'A' and resid 577 through 591 Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 599 through 616 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 631 Processing helix chain 'A' and resid 634 through 652 Processing helix chain 'A' and resid 656 through 671 Processing helix chain 'A' and resid 675 through 694 Processing helix chain 'A' and resid 705 through 720 Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 726 through 761 removed outlier: 3.572A pdb=" N LEU A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ASP A 732 " --> pdb=" O ASP A 728 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ALA A 735 " --> pdb=" O LEU A 731 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 761 " --> pdb=" O ASP A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 782 Processing helix chain 'A' and resid 785 through 791 removed outlier: 3.529A pdb=" N ASN A 789 " --> pdb=" O PHE A 785 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 790 " --> pdb=" O LEU A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 817 removed outlier: 4.276A pdb=" N ALA A 799 " --> pdb=" O ALA A 795 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N CYS A 803 " --> pdb=" O ALA A 799 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU A 804 " --> pdb=" O GLN A 800 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS A 817 " --> pdb=" O GLU A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 843 removed outlier: 3.827A pdb=" N THR A 829 " --> pdb=" O CYS A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 863 Processing helix chain 'A' and resid 865 through 884 removed outlier: 3.695A pdb=" N ALA A 869 " --> pdb=" O ASP A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 901 removed outlier: 3.883A pdb=" N GLN A 890 " --> pdb=" O PRO A 886 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A 891 " --> pdb=" O SER A 887 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N HIS A 892 " --> pdb=" O TYR A 888 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS A 901 " --> pdb=" O ALA A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 928 Processing helix chain 'A' and resid 930 through 944 removed outlier: 3.707A pdb=" N SER A 936 " --> pdb=" O THR A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 949 Processing helix chain 'A' and resid 951 through 969 removed outlier: 3.603A pdb=" N LEU A 956 " --> pdb=" O LYS A 952 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 957 " --> pdb=" O ALA A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 986 removed outlier: 3.675A pdb=" N GLU A 982 " --> pdb=" O HIS A 978 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 983 " --> pdb=" O SER A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.552A pdb=" N ALA A 995 " --> pdb=" O THR A 991 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A1010 " --> pdb=" O ILE A1006 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY A1012 " --> pdb=" O LEU A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1059 removed outlier: 4.148A pdb=" N VAL A1035 " --> pdb=" O GLY A1031 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TRP A1038 " --> pdb=" O LEU A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1079 Processing helix chain 'A' and resid 1080 through 1098 removed outlier: 3.543A pdb=" N CYS A1084 " --> pdb=" O ILE A1080 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A1086 " --> pdb=" O ARG A1082 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A1097 " --> pdb=" O GLU A1093 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A1098 " --> pdb=" O LEU A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1119 Processing helix chain 'A' and resid 1194 through 1199 removed outlier: 4.067A pdb=" N LEU A1197 " --> pdb=" O PRO A1194 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS A1199 " --> pdb=" O PHE A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1210 removed outlier: 3.520A pdb=" N SER A1210 " --> pdb=" O SER A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1231 Processing helix chain 'A' and resid 1236 through 1264 Proline residue: A1249 - end of helix Processing helix chain 'A' and resid 1274 through 1294 removed outlier: 4.139A pdb=" N GLU A1278 " --> pdb=" O SER A1274 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASN A1293 " --> pdb=" O LEU A1289 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A1294 " --> pdb=" O GLU A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1301 removed outlier: 3.665A pdb=" N LEU A1300 " --> pdb=" O ASN A1297 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1314 removed outlier: 4.138A pdb=" N ARG A1314 " --> pdb=" O PHE A1310 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1317 No H-bonds generated for 'chain 'A' and resid 1315 through 1317' Processing helix chain 'A' and resid 1318 through 1335 removed outlier: 3.872A pdb=" N GLY A1335 " --> pdb=" O LEU A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1346 removed outlier: 3.601A pdb=" N PHE A1345 " --> pdb=" O THR A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1646 removed outlier: 3.686A pdb=" N ILE A1645 " --> pdb=" O ALA A1641 " (cutoff:3.500A) Processing helix chain 'A' and resid 1652 through 1666 removed outlier: 3.757A pdb=" N HIS A1656 " --> pdb=" O GLY A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1679 Processing helix chain 'A' and resid 1682 through 1701 removed outlier: 3.649A pdb=" N ARG A1686 " --> pdb=" O SER A1682 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A1701 " --> pdb=" O LEU A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1725 through 1735 Processing helix chain 'A' and resid 1745 through 1757 Processing helix chain 'A' and resid 1806 through 1826 removed outlier: 3.901A pdb=" N SER A1826 " --> pdb=" O LYS A1822 " (cutoff:3.500A) Processing helix chain 'A' and resid 1829 through 1855 removed outlier: 3.697A pdb=" N TRP A1833 " --> pdb=" O ASP A1829 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A1852 " --> pdb=" O ILE A1848 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A1855 " --> pdb=" O LEU A1851 " (cutoff:3.500A) Processing helix chain 'A' and resid 1856 through 1864 removed outlier: 3.618A pdb=" N LYS A1860 " --> pdb=" O GLY A1857 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY A1861 " --> pdb=" O CYS A1858 " (cutoff:3.500A) Processing helix chain 'A' and resid 1871 through 1887 removed outlier: 3.983A pdb=" N ASP A1885 " --> pdb=" O GLU A1881 " (cutoff:3.500A) Processing helix chain 'A' and resid 1892 through 1901 removed outlier: 3.650A pdb=" N LEU A1896 " --> pdb=" O ASP A1892 " (cutoff:3.500A) Processing helix chain 'A' and resid 1907 through 1919 Processing helix chain 'A' and resid 1922 through 1938 removed outlier: 3.521A pdb=" N ALA A1926 " --> pdb=" O GLN A1922 " (cutoff:3.500A) Processing helix chain 'A' and resid 1960 through 1964 Processing helix chain 'A' and resid 1977 through 1990 removed outlier: 4.221A pdb=" N LEU A1981 " --> pdb=" O SER A1977 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A1982 " --> pdb=" O PHE A1978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1994 through 1999 Processing helix chain 'A' and resid 2016 through 2028 removed outlier: 4.795A pdb=" N ALA A2024 " --> pdb=" O GLU A2020 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASN A2025 " --> pdb=" O GLN A2021 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A2028 " --> pdb=" O ALA A2024 " (cutoff:3.500A) Processing helix chain 'A' and resid 2041 through 2051 removed outlier: 3.632A pdb=" N VAL A2045 " --> pdb=" O ARG A2041 " (cutoff:3.500A) Processing helix chain 'A' and resid 2068 through 2074 Processing helix chain 'A' and resid 2101 through 2109 removed outlier: 3.809A pdb=" N LYS A2105 " --> pdb=" O GLY A2101 " (cutoff:3.500A) Processing helix chain 'A' and resid 2125 through 2139 Processing helix chain 'A' and resid 2145 through 2153 removed outlier: 3.907A pdb=" N TYR A2149 " --> pdb=" O PRO A2145 " (cutoff:3.500A) Processing helix chain 'A' and resid 2154 through 2156 No H-bonds generated for 'chain 'A' and resid 2154 through 2156' Processing sheet with id=AA1, first strand: chain 'A' and resid 1791 through 1799 removed outlier: 5.869A pdb=" N GLU A1788 " --> pdb=" O PRO A1792 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR A1781 " --> pdb=" O ALA A1771 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2032 through 2036 removed outlier: 5.935A pdb=" N THR A2005 " --> pdb=" O ARG A2033 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL A2035 " --> pdb=" O THR A2005 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TYR A2007 " --> pdb=" O VAL A2035 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR A2055 " --> pdb=" O LEU A2082 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA A2081 " --> pdb=" O LEU A2115 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N ASN A2117 " --> pdb=" O ALA A2081 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N LEU A2083 " --> pdb=" O ASN A2117 " (cutoff:3.500A) 722 hydrogen bonds defined for protein. 2130 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: 1.53 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3480 1.34 - 1.46: 1497 1.46 - 1.58: 5481 1.58 - 1.69: 1 1.69 - 1.81: 58 Bond restraints: 10517 Sorted by residual: bond pdb=" N GLU A 601 " pdb=" CA GLU A 601 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 8.94e+00 bond pdb=" N VAL A 547 " pdb=" CA VAL A 547 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.30e-02 5.92e+03 8.87e+00 bond pdb=" N VAL A 859 " pdb=" CA VAL A 859 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 7.97e+00 bond pdb=" N ILE A 858 " pdb=" CA ILE A 858 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.14e-02 7.69e+03 7.95e+00 bond pdb=" N ASP A 773 " pdb=" CA ASP A 773 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.16e-02 7.43e+03 7.81e+00 ... (remaining 10512 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 13934 2.02 - 4.03: 339 4.03 - 6.05: 35 6.05 - 8.06: 13 8.06 - 10.08: 1 Bond angle restraints: 14322 Sorted by residual: angle pdb=" N PRO A 331 " pdb=" CA PRO A 331 " pdb=" CB PRO A 331 " ideal model delta sigma weight residual 103.08 110.15 -7.07 9.70e-01 1.06e+00 5.32e+01 angle pdb=" N PRO A 329 " pdb=" CA PRO A 329 " pdb=" CB PRO A 329 " ideal model delta sigma weight residual 103.00 110.35 -7.35 1.10e+00 8.26e-01 4.47e+01 angle pdb=" N PRO A 332 " pdb=" CA PRO A 332 " pdb=" CB PRO A 332 " ideal model delta sigma weight residual 103.33 110.28 -6.95 1.10e+00 8.26e-01 3.99e+01 angle pdb=" C LEU A 976 " pdb=" CA LEU A 976 " pdb=" CB LEU A 976 " ideal model delta sigma weight residual 116.54 109.60 6.94 1.15e+00 7.56e-01 3.65e+01 angle pdb=" CG ARG A1831 " pdb=" CD ARG A1831 " pdb=" NE ARG A1831 " ideal model delta sigma weight residual 112.00 122.08 -10.08 2.20e+00 2.07e-01 2.10e+01 ... (remaining 14317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.90: 5627 15.90 - 31.79: 516 31.79 - 47.69: 141 47.69 - 63.58: 54 63.58 - 79.48: 11 Dihedral angle restraints: 6349 sinusoidal: 2305 harmonic: 4044 Sorted by residual: dihedral pdb=" CB CYS A 694 " pdb=" SG CYS A 694 " pdb=" SG CYS A 744 " pdb=" CB CYS A 744 " ideal model delta sinusoidal sigma weight residual -86.00 -165.48 79.48 1 1.00e+01 1.00e-02 7.85e+01 dihedral pdb=" CA LEU A 730 " pdb=" C LEU A 730 " pdb=" N LEU A 731 " pdb=" CA LEU A 731 " ideal model delta harmonic sigma weight residual 180.00 160.18 19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA LEU A2075 " pdb=" C LEU A2075 " pdb=" N SER A2076 " pdb=" CA SER A2076 " ideal model delta harmonic sigma weight residual 180.00 161.72 18.28 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 6346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1367 0.046 - 0.093: 259 0.093 - 0.139: 56 0.139 - 0.186: 6 0.186 - 0.232: 6 Chirality restraints: 1694 Sorted by residual: chirality pdb=" CA PRO A 329 " pdb=" N PRO A 329 " pdb=" C PRO A 329 " pdb=" CB PRO A 329 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PRO A 332 " pdb=" N PRO A 332 " pdb=" C PRO A 332 " pdb=" CB PRO A 332 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA PRO A 331 " pdb=" N PRO A 331 " pdb=" C PRO A 331 " pdb=" CB PRO A 331 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1691 not shown) Planarity restraints: 1850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 732 " 0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ASP A 732 " -0.061 2.00e-02 2.50e+03 pdb=" O ASP A 732 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP A 733 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 862 " 0.249 9.50e-02 1.11e+02 1.12e-01 7.68e+00 pdb=" NE ARG A 862 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 862 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 862 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 862 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A1871 " 0.034 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO A1872 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A1872 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1872 " 0.029 5.00e-02 4.00e+02 ... (remaining 1847 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 52 2.56 - 3.15: 8303 3.15 - 3.73: 16291 3.73 - 4.32: 19793 4.32 - 4.90: 34268 Nonbonded interactions: 78707 Sorted by model distance: nonbonded pdb=" OG SER A 595 " pdb=" OE1 GLU A 597 " model vdw 1.980 3.040 nonbonded pdb=" OG SER A1200 " pdb=" O THR A1202 " model vdw 2.183 3.040 nonbonded pdb=" N GLU A1032 " pdb=" OE1 GLU A1032 " model vdw 2.202 3.120 nonbonded pdb=" N GLN A1701 " pdb=" OE1 GLN A1701 " model vdw 2.223 3.120 nonbonded pdb=" OH TYR A 888 " pdb=" OE1 GLN A1260 " model vdw 2.248 3.040 ... (remaining 78702 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.120 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.004 0.120 10522 Z= 0.258 Angle : 0.715 10.081 14327 Z= 0.449 Chirality : 0.041 0.232 1694 Planarity : 0.005 0.112 1850 Dihedral : 14.812 77.961 3722 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.10 % Allowed : 14.88 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 (0.23), residues: 1384 helix: 2.25 (0.17), residues: 919 sheet: 2.65 (0.72), residues: 48 loop : -1.60 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 759 TYR 0.012 0.001 TYR A1030 PHE 0.034 0.002 PHE A 792 TRP 0.012 0.001 TRP A 740 HIS 0.004 0.001 HIS A1656 Details of bonding type rmsd covalent geometry : bond 0.00428 (10517) covalent geometry : angle 0.71477 (14322) SS BOND : bond 0.00497 ( 1) SS BOND : angle 0.34111 ( 2) hydrogen bonds : bond 0.15708 ( 722) hydrogen bonds : angle 4.82241 ( 2130) metal coordination : bond 0.01412 ( 4) metal coordination : angle 0.91462 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 991 THR cc_start: 0.8932 (t) cc_final: 0.8600 (p) REVERT: A 1321 TRP cc_start: 0.8023 (m-90) cc_final: 0.7813 (m-90) REVERT: A 1353 PRO cc_start: 0.8246 (Cg_exo) cc_final: 0.7977 (Cg_endo) REVERT: A 1657 LEU cc_start: 0.8614 (mp) cc_final: 0.8339 (mt) REVERT: A 1829 ASP cc_start: 0.7229 (t0) cc_final: 0.6934 (t0) REVERT: A 2019 GLU cc_start: 0.7135 (tp30) cc_final: 0.6839 (tp30) REVERT: A 2054 LEU cc_start: 0.9077 (tp) cc_final: 0.8765 (tp) REVERT: A 2124 ARG cc_start: 0.8371 (mmm-85) cc_final: 0.8036 (tpp80) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.1426 time to fit residues: 32.4154 Evaluate side-chains 122 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 ASN A 781 GLN A 800 GLN A 923 GLN A1301 GLN A1656 HIS A1938 GLN ** A2060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2094 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.060338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.050900 restraints weight = 38038.605| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.58 r_work: 0.2802 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10522 Z= 0.144 Angle : 0.584 8.399 14327 Z= 0.303 Chirality : 0.037 0.137 1694 Planarity : 0.005 0.050 1850 Dihedral : 4.049 18.874 1481 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.85 % Allowed : 14.40 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 2.08 (0.23), residues: 1384 helix: 2.47 (0.17), residues: 931 sheet: 2.66 (0.74), residues: 48 loop : -1.56 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 727 TYR 0.015 0.002 TYR A2057 PHE 0.031 0.002 PHE A 792 TRP 0.011 0.001 TRP A 740 HIS 0.005 0.001 HIS A1656 Details of bonding type rmsd covalent geometry : bond 0.00313 (10517) covalent geometry : angle 0.58334 (14322) SS BOND : bond 0.00546 ( 1) SS BOND : angle 0.70404 ( 2) hydrogen bonds : bond 0.05177 ( 722) hydrogen bonds : angle 3.90253 ( 2130) metal coordination : bond 0.01426 ( 4) metal coordination : angle 2.44217 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 611 MET cc_start: 0.8358 (mmm) cc_final: 0.8016 (mmm) REVERT: A 797 ASP cc_start: 0.7986 (p0) cc_final: 0.7737 (p0) REVERT: A 913 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8816 (mm) REVERT: A 1120 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7160 (mp0) REVERT: A 1231 MET cc_start: 0.9028 (ttm) cc_final: 0.8798 (ttm) REVERT: A 1234 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: A 1321 TRP cc_start: 0.8256 (m-90) cc_final: 0.8007 (m-90) REVERT: A 1351 TRP cc_start: 0.8377 (t60) cc_final: 0.7996 (t60) REVERT: A 2019 GLU cc_start: 0.8085 (tp30) cc_final: 0.7604 (tp30) REVERT: A 2039 VAL cc_start: 0.8437 (t) cc_final: 0.8095 (p) REVERT: A 2054 LEU cc_start: 0.9164 (tp) cc_final: 0.8868 (tp) REVERT: A 2124 ARG cc_start: 0.8763 (mmm-85) cc_final: 0.8390 (mmm-85) outliers start: 19 outliers final: 12 residues processed: 152 average time/residue: 0.1136 time to fit residues: 22.8659 Evaluate side-chains 142 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1030 TYR Chi-restraints excluded: chain A residue 1234 GLN Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1743 HIS Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1806 HIS Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1937 LEU Chi-restraints excluded: chain A residue 1988 LYS Chi-restraints excluded: chain A residue 2097 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 80 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 136 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 841 GLN A1343 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.059387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.049856 restraints weight = 37924.492| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.59 r_work: 0.2774 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10522 Z= 0.135 Angle : 0.547 7.616 14327 Z= 0.282 Chirality : 0.037 0.158 1694 Planarity : 0.005 0.052 1850 Dihedral : 3.950 18.592 1481 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.63 % Allowed : 15.08 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 2.23 (0.23), residues: 1384 helix: 2.59 (0.17), residues: 934 sheet: 2.53 (0.75), residues: 48 loop : -1.51 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 758 TYR 0.013 0.001 TYR A2161 PHE 0.023 0.002 PHE A 792 TRP 0.011 0.001 TRP A 740 HIS 0.002 0.001 HIS A1694 Details of bonding type rmsd covalent geometry : bond 0.00296 (10517) covalent geometry : angle 0.54618 (14322) SS BOND : bond 0.00490 ( 1) SS BOND : angle 0.72557 ( 2) hydrogen bonds : bond 0.04767 ( 722) hydrogen bonds : angle 3.72589 ( 2130) metal coordination : bond 0.01736 ( 4) metal coordination : angle 2.06428 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 611 MET cc_start: 0.8409 (mmm) cc_final: 0.7805 (mmm) REVERT: A 797 ASP cc_start: 0.8049 (p0) cc_final: 0.7644 (p0) REVERT: A 895 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7837 (tp30) REVERT: A 913 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8776 (mm) REVERT: A 968 TYR cc_start: 0.7536 (m-80) cc_final: 0.7154 (m-80) REVERT: A 1030 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.7595 (t80) REVERT: A 1120 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7235 (mp0) REVERT: A 1234 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8385 (tt0) REVERT: A 1321 TRP cc_start: 0.8310 (m-90) cc_final: 0.8044 (m-90) REVERT: A 1351 TRP cc_start: 0.8328 (t60) cc_final: 0.7915 (t60) REVERT: A 1878 ARG cc_start: 0.8199 (mtm110) cc_final: 0.7976 (mtm110) REVERT: A 2019 GLU cc_start: 0.8118 (tp30) cc_final: 0.7602 (tp30) REVERT: A 2039 VAL cc_start: 0.8474 (t) cc_final: 0.8102 (p) REVERT: A 2054 LEU cc_start: 0.9218 (tp) cc_final: 0.8945 (tp) outliers start: 27 outliers final: 12 residues processed: 158 average time/residue: 0.1372 time to fit residues: 28.7721 Evaluate side-chains 134 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1030 TYR Chi-restraints excluded: chain A residue 1234 GLN Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1667 HIS Chi-restraints excluded: chain A residue 1743 HIS Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1806 HIS Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1937 LEU Chi-restraints excluded: chain A residue 1988 LYS Chi-restraints excluded: chain A residue 2097 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.6980 chunk 135 optimal weight: 0.2980 chunk 96 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 127 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1343 GLN A2010 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.058851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.049279 restraints weight = 37668.194| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.56 r_work: 0.2758 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10522 Z= 0.133 Angle : 0.536 6.999 14327 Z= 0.276 Chirality : 0.037 0.188 1694 Planarity : 0.005 0.050 1850 Dihedral : 3.907 18.694 1481 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.53 % Allowed : 15.95 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 2.19 (0.23), residues: 1384 helix: 2.57 (0.17), residues: 939 sheet: 2.46 (0.76), residues: 48 loop : -1.61 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A2023 TYR 0.017 0.001 TYR A2161 PHE 0.031 0.002 PHE A 792 TRP 0.012 0.001 TRP A 633 HIS 0.003 0.001 HIS A1694 Details of bonding type rmsd covalent geometry : bond 0.00294 (10517) covalent geometry : angle 0.53501 (14322) SS BOND : bond 0.00475 ( 1) SS BOND : angle 0.70138 ( 2) hydrogen bonds : bond 0.04633 ( 722) hydrogen bonds : angle 3.65999 ( 2130) metal coordination : bond 0.01796 ( 4) metal coordination : angle 2.13820 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 611 MET cc_start: 0.8521 (mmm) cc_final: 0.7616 (mmm) REVERT: A 615 ARG cc_start: 0.8939 (mmt90) cc_final: 0.8638 (mmt90) REVERT: A 797 ASP cc_start: 0.8145 (p0) cc_final: 0.7768 (p0) REVERT: A 913 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8798 (mm) REVERT: A 1030 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.7615 (t80) REVERT: A 1120 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7147 (mp0) REVERT: A 1234 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8458 (tt0) REVERT: A 1321 TRP cc_start: 0.8362 (m-90) cc_final: 0.8090 (m-90) REVERT: A 1351 TRP cc_start: 0.8339 (t60) cc_final: 0.7956 (t60) REVERT: A 1874 GLN cc_start: 0.8387 (tt0) cc_final: 0.8132 (tt0) REVERT: A 2019 GLU cc_start: 0.8093 (tp30) cc_final: 0.7600 (tp30) REVERT: A 2054 LEU cc_start: 0.9235 (tp) cc_final: 0.8981 (tp) outliers start: 26 outliers final: 15 residues processed: 147 average time/residue: 0.1347 time to fit residues: 26.2835 Evaluate side-chains 139 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1030 TYR Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1234 GLN Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1667 HIS Chi-restraints excluded: chain A residue 1743 HIS Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1806 HIS Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1937 LEU Chi-restraints excluded: chain A residue 2045 VAL Chi-restraints excluded: chain A residue 2097 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 62 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 112 optimal weight: 0.4980 chunk 85 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 ASN A1265 HIS A1343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.058718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.049170 restraints weight = 37880.654| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.57 r_work: 0.2756 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10522 Z= 0.131 Angle : 0.542 6.872 14327 Z= 0.280 Chirality : 0.037 0.155 1694 Planarity : 0.004 0.051 1850 Dihedral : 3.902 18.577 1481 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.53 % Allowed : 17.41 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 2.22 (0.23), residues: 1384 helix: 2.61 (0.17), residues: 936 sheet: 2.41 (0.77), residues: 48 loop : -1.59 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 759 TYR 0.016 0.001 TYR A2161 PHE 0.016 0.001 PHE A 792 TRP 0.010 0.001 TRP A 740 HIS 0.006 0.001 HIS A1265 Details of bonding type rmsd covalent geometry : bond 0.00292 (10517) covalent geometry : angle 0.54129 (14322) SS BOND : bond 0.00440 ( 1) SS BOND : angle 0.66993 ( 2) hydrogen bonds : bond 0.04532 ( 722) hydrogen bonds : angle 3.62742 ( 2130) metal coordination : bond 0.01843 ( 4) metal coordination : angle 2.26748 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 611 MET cc_start: 0.8641 (mmm) cc_final: 0.7618 (mmm) REVERT: A 615 ARG cc_start: 0.8967 (mmt90) cc_final: 0.8658 (mmt90) REVERT: A 621 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9048 (tp) REVERT: A 797 ASP cc_start: 0.8100 (p0) cc_final: 0.7774 (p0) REVERT: A 913 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8797 (mm) REVERT: A 923 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8754 (mm-40) REVERT: A 1120 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7006 (mp0) REVERT: A 1234 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8455 (tt0) REVERT: A 1321 TRP cc_start: 0.8396 (m-90) cc_final: 0.8128 (m-90) REVERT: A 1351 TRP cc_start: 0.8439 (t60) cc_final: 0.7958 (t60) REVERT: A 1874 GLN cc_start: 0.8471 (tt0) cc_final: 0.8241 (tt0) REVERT: A 2019 GLU cc_start: 0.8163 (tp30) cc_final: 0.7674 (tp30) REVERT: A 2054 LEU cc_start: 0.9249 (tp) cc_final: 0.9005 (tp) REVERT: A 2118 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8665 (tp) outliers start: 26 outliers final: 13 residues processed: 149 average time/residue: 0.1322 time to fit residues: 26.1349 Evaluate side-chains 137 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1234 GLN Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1667 HIS Chi-restraints excluded: chain A residue 1743 HIS Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1806 HIS Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1937 LEU Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2118 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 5 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 79 optimal weight: 0.0980 chunk 33 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 129 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.058572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.048967 restraints weight = 38266.546| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.59 r_work: 0.2749 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10522 Z= 0.132 Angle : 0.547 6.819 14327 Z= 0.282 Chirality : 0.036 0.142 1694 Planarity : 0.004 0.052 1850 Dihedral : 3.885 19.215 1481 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.92 % Allowed : 17.12 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 2.25 (0.23), residues: 1384 helix: 2.62 (0.17), residues: 940 sheet: 2.37 (0.78), residues: 48 loop : -1.58 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 759 TYR 0.012 0.001 TYR A2161 PHE 0.032 0.002 PHE A 792 TRP 0.010 0.001 TRP A 740 HIS 0.009 0.001 HIS A1265 Details of bonding type rmsd covalent geometry : bond 0.00297 (10517) covalent geometry : angle 0.54603 (14322) SS BOND : bond 0.00427 ( 1) SS BOND : angle 0.66310 ( 2) hydrogen bonds : bond 0.04467 ( 722) hydrogen bonds : angle 3.60396 ( 2130) metal coordination : bond 0.01780 ( 4) metal coordination : angle 2.30673 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 611 MET cc_start: 0.8717 (mmm) cc_final: 0.7487 (mmm) REVERT: A 615 ARG cc_start: 0.8982 (mmt90) cc_final: 0.8728 (mmt90) REVERT: A 793 ASN cc_start: 0.7086 (p0) cc_final: 0.6878 (p0) REVERT: A 797 ASP cc_start: 0.8094 (p0) cc_final: 0.7757 (p0) REVERT: A 913 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8817 (mm) REVERT: A 1120 GLU cc_start: 0.7398 (mt-10) cc_final: 0.6937 (mp0) REVERT: A 1234 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8450 (tt0) REVERT: A 1321 TRP cc_start: 0.8398 (m-90) cc_final: 0.8138 (m-90) REVERT: A 1351 TRP cc_start: 0.8394 (t60) cc_final: 0.7962 (t60) REVERT: A 1874 GLN cc_start: 0.8477 (tt0) cc_final: 0.8247 (tt0) REVERT: A 2054 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9021 (tp) outliers start: 30 outliers final: 18 residues processed: 148 average time/residue: 0.1298 time to fit residues: 25.6573 Evaluate side-chains 139 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 840 TYR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1030 TYR Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1234 GLN Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1667 HIS Chi-restraints excluded: chain A residue 1743 HIS Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1806 HIS Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1937 LEU Chi-restraints excluded: chain A residue 2045 VAL Chi-restraints excluded: chain A residue 2054 LEU Chi-restraints excluded: chain A residue 2097 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 138 optimal weight: 0.0670 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 101 optimal weight: 0.0570 chunk 97 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.059100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.049562 restraints weight = 37698.734| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.57 r_work: 0.2768 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10522 Z= 0.121 Angle : 0.545 7.128 14327 Z= 0.281 Chirality : 0.036 0.135 1694 Planarity : 0.004 0.054 1850 Dihedral : 3.843 19.736 1481 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.11 % Allowed : 16.83 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 2.35 (0.23), residues: 1384 helix: 2.70 (0.17), residues: 940 sheet: 2.35 (0.77), residues: 48 loop : -1.57 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2074 TYR 0.010 0.001 TYR A2161 PHE 0.014 0.001 PHE A 792 TRP 0.011 0.001 TRP A 740 HIS 0.005 0.001 HIS A1265 Details of bonding type rmsd covalent geometry : bond 0.00268 (10517) covalent geometry : angle 0.54452 (14322) SS BOND : bond 0.00331 ( 1) SS BOND : angle 0.51955 ( 2) hydrogen bonds : bond 0.04114 ( 722) hydrogen bonds : angle 3.51938 ( 2130) metal coordination : bond 0.01576 ( 4) metal coordination : angle 2.06705 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 611 MET cc_start: 0.8749 (mmm) cc_final: 0.7490 (mmm) REVERT: A 797 ASP cc_start: 0.8072 (p0) cc_final: 0.7722 (p0) REVERT: A 895 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7924 (tp30) REVERT: A 913 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8842 (mm) REVERT: A 923 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8718 (mm110) REVERT: A 1120 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6567 (mp0) REVERT: A 1234 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8445 (tt0) REVERT: A 1266 LYS cc_start: 0.9255 (mmmm) cc_final: 0.9051 (mmmm) REVERT: A 1321 TRP cc_start: 0.8351 (m-90) cc_final: 0.8109 (m-90) REVERT: A 1351 TRP cc_start: 0.8382 (t60) cc_final: 0.7963 (t60) REVERT: A 1874 GLN cc_start: 0.8491 (tt0) cc_final: 0.8241 (tt0) REVERT: A 1878 ARG cc_start: 0.8249 (mtm110) cc_final: 0.8013 (mtm110) REVERT: A 2054 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9029 (tp) REVERT: A 2118 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8689 (tp) outliers start: 32 outliers final: 18 residues processed: 152 average time/residue: 0.1243 time to fit residues: 24.7670 Evaluate side-chains 141 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 840 TYR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1234 GLN Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1667 HIS Chi-restraints excluded: chain A residue 1743 HIS Chi-restraints excluded: chain A residue 1806 HIS Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1937 LEU Chi-restraints excluded: chain A residue 2045 VAL Chi-restraints excluded: chain A residue 2054 LEU Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2118 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 92 optimal weight: 0.4980 chunk 98 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 123 optimal weight: 0.0370 chunk 129 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.058733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.049095 restraints weight = 38097.043| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.62 r_work: 0.2751 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10522 Z= 0.133 Angle : 0.583 7.491 14327 Z= 0.301 Chirality : 0.038 0.296 1694 Planarity : 0.004 0.054 1850 Dihedral : 3.902 24.884 1481 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.72 % Allowed : 17.70 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 2.28 (0.23), residues: 1384 helix: 2.66 (0.17), residues: 940 sheet: 2.37 (0.77), residues: 48 loop : -1.61 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2023 TYR 0.009 0.001 TYR A2161 PHE 0.041 0.002 PHE A 792 TRP 0.010 0.001 TRP A 740 HIS 0.004 0.001 HIS A1265 Details of bonding type rmsd covalent geometry : bond 0.00302 (10517) covalent geometry : angle 0.58175 (14322) SS BOND : bond 0.00388 ( 1) SS BOND : angle 0.60339 ( 2) hydrogen bonds : bond 0.04306 ( 722) hydrogen bonds : angle 3.57466 ( 2130) metal coordination : bond 0.01738 ( 4) metal coordination : angle 2.23773 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 611 MET cc_start: 0.8569 (mmm) cc_final: 0.7591 (mmm) REVERT: A 797 ASP cc_start: 0.8069 (p0) cc_final: 0.7831 (p0) REVERT: A 913 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8762 (mm) REVERT: A 923 GLN cc_start: 0.8956 (mm-40) cc_final: 0.8734 (mm-40) REVERT: A 1234 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8458 (tt0) REVERT: A 1301 GLN cc_start: 0.7915 (mt0) cc_final: 0.7564 (mm110) REVERT: A 1321 TRP cc_start: 0.8384 (m-90) cc_final: 0.8138 (m-90) REVERT: A 1351 TRP cc_start: 0.8351 (t60) cc_final: 0.7924 (t60) REVERT: A 1874 GLN cc_start: 0.8570 (tt0) cc_final: 0.8368 (tm-30) REVERT: A 2054 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9042 (tp) REVERT: A 2118 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8681 (tp) outliers start: 28 outliers final: 20 residues processed: 142 average time/residue: 0.1383 time to fit residues: 26.0002 Evaluate side-chains 144 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 840 TYR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1234 GLN Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1667 HIS Chi-restraints excluded: chain A residue 1743 HIS Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1806 HIS Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1937 LEU Chi-restraints excluded: chain A residue 2045 VAL Chi-restraints excluded: chain A residue 2054 LEU Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2118 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 48 optimal weight: 0.0770 chunk 25 optimal weight: 0.9990 chunk 126 optimal weight: 0.0050 chunk 83 optimal weight: 0.3980 chunk 82 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 91 optimal weight: 0.0000 chunk 89 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1294 GLN A1343 GLN ** A2010 ASN ** 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 = 0.3190 r_free = 0.3190 target = 0.060260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.050628 restraints weight = 37897.118| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.60 r_work: 0.2798 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10522 Z= 0.115 Angle : 0.565 8.332 14327 Z= 0.291 Chirality : 0.036 0.186 1694 Planarity : 0.004 0.056 1850 Dihedral : 3.840 26.392 1481 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.82 % Allowed : 17.70 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 2.39 (0.23), residues: 1384 helix: 2.75 (0.17), residues: 940 sheet: 2.38 (0.78), residues: 48 loop : -1.59 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1831 TYR 0.016 0.001 TYR A1916 PHE 0.029 0.001 PHE A 792 TRP 0.011 0.001 TRP A 740 HIS 0.004 0.000 HIS A1265 Details of bonding type rmsd covalent geometry : bond 0.00254 (10517) covalent geometry : angle 0.56506 (14322) SS BOND : bond 0.00212 ( 1) SS BOND : angle 0.38379 ( 2) hydrogen bonds : bond 0.03673 ( 722) hydrogen bonds : angle 3.45992 ( 2130) metal coordination : bond 0.01134 ( 4) metal coordination : angle 1.66905 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 611 MET cc_start: 0.8624 (mmm) cc_final: 0.7912 (mmm) REVERT: A 797 ASP cc_start: 0.8044 (p0) cc_final: 0.7758 (p0) REVERT: A 895 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7918 (tp30) REVERT: A 913 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8769 (mm) REVERT: A 1030 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.7663 (t80) REVERT: A 1234 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8417 (tt0) REVERT: A 1301 GLN cc_start: 0.7906 (mt0) cc_final: 0.7606 (mm110) REVERT: A 1321 TRP cc_start: 0.8326 (m-90) cc_final: 0.8101 (m-90) REVERT: A 1351 TRP cc_start: 0.8386 (t60) cc_final: 0.7958 (t60) REVERT: A 1874 GLN cc_start: 0.8536 (tt0) cc_final: 0.8282 (tm-30) REVERT: A 1878 ARG cc_start: 0.8047 (mtm110) cc_final: 0.7736 (mtm110) REVERT: A 2118 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8663 (tp) outliers start: 29 outliers final: 17 residues processed: 148 average time/residue: 0.1372 time to fit residues: 26.8740 Evaluate side-chains 140 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 840 TYR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1030 TYR Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1234 GLN Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1667 HIS Chi-restraints excluded: chain A residue 1743 HIS Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1806 HIS Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1937 LEU Chi-restraints excluded: chain A residue 2045 VAL Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 62 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 92 optimal weight: 0.0050 chunk 22 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 HIS A1343 GLN A2010 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.058621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.048865 restraints weight = 37591.851| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.60 r_work: 0.2744 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10522 Z= 0.145 Angle : 0.612 8.698 14327 Z= 0.316 Chirality : 0.038 0.185 1694 Planarity : 0.005 0.054 1850 Dihedral : 3.921 26.237 1481 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.24 % Allowed : 18.19 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 2.30 (0.23), residues: 1384 helix: 2.67 (0.17), residues: 940 sheet: 2.27 (0.79), residues: 48 loop : -1.59 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1831 TYR 0.010 0.001 TYR A2161 PHE 0.018 0.002 PHE A1345 TRP 0.009 0.001 TRP A 740 HIS 0.003 0.001 HIS A1265 Details of bonding type rmsd covalent geometry : bond 0.00335 (10517) covalent geometry : angle 0.61117 (14322) SS BOND : bond 0.00484 ( 1) SS BOND : angle 0.71466 ( 2) hydrogen bonds : bond 0.04483 ( 722) hydrogen bonds : angle 3.58305 ( 2130) metal coordination : bond 0.01945 ( 4) metal coordination : angle 2.38316 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 611 MET cc_start: 0.8622 (mmm) cc_final: 0.8021 (mmm) REVERT: A 797 ASP cc_start: 0.8069 (p0) cc_final: 0.7821 (p0) REVERT: A 913 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8768 (mm) REVERT: A 923 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8649 (mm-40) REVERT: A 1030 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7752 (t80) REVERT: A 1234 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8416 (tt0) REVERT: A 1301 GLN cc_start: 0.7945 (mt0) cc_final: 0.7619 (mm110) REVERT: A 1321 TRP cc_start: 0.8424 (m-90) cc_final: 0.8168 (m-90) REVERT: A 1351 TRP cc_start: 0.8360 (t60) cc_final: 0.7901 (t60) REVERT: A 1874 GLN cc_start: 0.8562 (tt0) cc_final: 0.8305 (tt0) REVERT: A 2118 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8672 (tp) outliers start: 23 outliers final: 16 residues processed: 135 average time/residue: 0.1429 time to fit residues: 25.5477 Evaluate side-chains 139 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 840 TYR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1030 TYR Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1234 GLN Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1667 HIS Chi-restraints excluded: chain A residue 1743 HIS Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1806 HIS Chi-restraints excluded: chain A residue 1882 LEU Chi-restraints excluded: chain A residue 1937 LEU Chi-restraints excluded: chain A residue 2045 VAL Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 22 optimal weight: 0.5980 chunk 112 optimal weight: 0.8980 chunk 53 optimal weight: 0.0570 chunk 98 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 62 optimal weight: 0.0170 chunk 110 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.059493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.049770 restraints weight = 37881.375| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.60 r_work: 0.2773 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10522 Z= 0.124 Angle : 0.593 8.418 14327 Z= 0.305 Chirality : 0.037 0.199 1694 Planarity : 0.004 0.055 1850 Dihedral : 3.876 26.318 1481 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.04 % Allowed : 18.58 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 2.33 (0.23), residues: 1384 helix: 2.68 (0.17), residues: 939 sheet: 2.24 (0.78), residues: 48 loop : -1.55 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1831 TYR 0.014 0.001 TYR A1916 PHE 0.026 0.002 PHE A 792 TRP 0.011 0.001 TRP A 740 HIS 0.003 0.001 HIS A1694 Details of bonding type rmsd covalent geometry : bond 0.00282 (10517) covalent geometry : angle 0.59189 (14322) SS BOND : bond 0.00320 ( 1) SS BOND : angle 0.48689 ( 2) hydrogen bonds : bond 0.04000 ( 722) hydrogen bonds : angle 3.50843 ( 2130) metal coordination : bond 0.01439 ( 4) metal coordination : angle 1.98756 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2010.59 seconds wall clock time: 35 minutes 20.69 seconds (2120.69 seconds total)