Starting phenix.real_space_refine on Wed Feb 4 20:19:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hn0_52303/02_2026/9hn0_52303.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hn0_52303/02_2026/9hn0_52303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hn0_52303/02_2026/9hn0_52303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hn0_52303/02_2026/9hn0_52303.map" model { file = "/net/cci-nas-00/data/ceres_data/9hn0_52303/02_2026/9hn0_52303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hn0_52303/02_2026/9hn0_52303.cif" } resolution = 2.8 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= -0.018 sd= 0.375 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 61 5.16 5 C 7898 2.51 5 N 2186 2.21 5 O 2320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s 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: 12466 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 2, 'TRANS': 5} Chain: "B" Number of atoms: 12399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1684, 12399 Classifications: {'peptide': 1684} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'PCIS': 2, 'PTRANS': 79, 'TRANS': 1602} Chain breaks: 5 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 701 Unresolved non-hydrogen angles: 895 Unresolved non-hydrogen dihedrals: 580 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'ARG:plan': 22, 'GLN:plan1': 10, 'ASP:plan': 10, 'ASN:plan1': 4, 'HIS:plan': 10, 'GLU:plan': 16, 'TYR:plan': 4, 'PHE:plan': 8, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 400 Chain: "B" 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 7213 SG CYS B1146 52.413 63.075 17.683 1.00 30.00 S ATOM 7227 SG CYS B1148 52.335 61.693 21.233 1.00 73.07 S ATOM 7247 SG CYS B1151 55.617 62.813 19.803 1.00 30.00 S Time building chain proxies: 2.78, per 1000 atoms: 0.22 Number of scatterers: 12466 At special positions: 0 Unit cell: (140.774, 194.918, 93.8496, 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 61 16.00 O 2320 8.00 N 2186 7.00 C 7898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 637 " - pdb=" SG CYS B 687 " 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: 1.09 Conformation dependent library (CDL) restraints added in 586.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B2201 " pdb="ZN ZN B2201 " - pdb=" ND1 HIS B1142 " pdb="ZN ZN B2201 " - pdb=" SG CYS B1148 " pdb="ZN ZN B2201 " - pdb=" SG CYS B1151 " pdb="ZN ZN B2201 " - pdb=" SG CYS B1146 " Number of angles added : 3 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 2 sheets defined 75.6% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'B' and resid 47 through 63 removed outlier: 3.724A pdb=" N ALA B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 89 Processing helix chain 'B' and resid 95 through 112 Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 123 through 132 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 144 through 158 Processing helix chain 'B' and resid 161 through 176 removed outlier: 3.905A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 205 Processing helix chain 'B' and resid 213 through 234 removed outlier: 3.610A pdb=" N LEU B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 265 Processing helix chain 'B' and resid 268 through 281 Processing helix chain 'B' and resid 287 through 304 removed outlier: 3.749A pdb=" N LEU B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 328 removed outlier: 4.296A pdb=" N VAL B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 350 removed outlier: 3.556A pdb=" N PHE B 342 " --> pdb=" O GLU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 380 removed outlier: 3.803A pdb=" N ILE B 360 " --> pdb=" O ARG B 356 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 414 removed outlier: 3.740A pdb=" N GLN B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 426 Processing helix chain 'B' and resid 426 through 442 removed outlier: 3.605A pdb=" N VAL B 434 " --> pdb=" O CYS B 430 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 470 Processing helix chain 'B' and resid 472 through 490 removed outlier: 3.588A pdb=" N ALA B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 478 " --> pdb=" O ALA B 474 " (cutoff:3.500A) Proline residue: B 482 - end of helix Processing helix chain 'B' and resid 499 through 518 removed outlier: 4.080A pdb=" N GLN B 510 " --> pdb=" O CYS B 506 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 534 removed outlier: 3.699A pdb=" N LYS B 525 " --> pdb=" O ALA B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 559 Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 568 through 573 removed outlier: 3.592A pdb=" N SER B 572 " --> pdb=" O THR B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 595 Processing helix chain 'B' and resid 599 through 614 Processing helix chain 'B' and resid 618 through 638 Processing helix chain 'B' and resid 641 through 646 Processing helix chain 'B' and resid 648 through 662 Processing helix chain 'B' and resid 669 through 704 Processing helix chain 'B' and resid 731 through 736 removed outlier: 4.075A pdb=" N ASN B 736 " --> pdb=" O ASN B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 760 removed outlier: 4.110A pdb=" N ALA B 741 " --> pdb=" O LEU B 737 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N CYS B 746 " --> pdb=" O ALA B 742 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU B 747 " --> pdb=" O GLN B 743 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS B 760 " --> pdb=" O GLU B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 removed outlier: 3.724A pdb=" N THR B 772 " --> pdb=" O CYS B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 807 Processing helix chain 'B' and resid 808 through 827 Processing helix chain 'B' and resid 828 through 843 Processing helix chain 'B' and resid 844 through 846 No H-bonds generated for 'chain 'B' and resid 844 through 846' Processing helix chain 'B' and resid 850 through 871 Processing helix chain 'B' and resid 873 through 886 Processing helix chain 'B' and resid 887 through 892 removed outlier: 3.508A pdb=" N GLN B 891 " --> pdb=" O PRO B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 913 removed outlier: 3.697A pdb=" N GLN B 903 " --> pdb=" O LEU B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 919 removed outlier: 6.096A pdb=" N ASN B 917 " --> pdb=" O LEU B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 929 Processing helix chain 'B' and resid 934 through 955 Processing helix chain 'B' and resid 974 through 1002 removed outlier: 3.743A pdb=" N VAL B 978 " --> pdb=" O GLY B 974 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1022 Processing helix chain 'B' and resid 1023 through 1041 Processing helix chain 'B' and resid 1043 through 1062 Processing helix chain 'B' and resid 1148 through 1153 Processing helix chain 'B' and resid 1153 through 1174 Processing helix chain 'B' and resid 1179 through 1207 Proline residue: B1192 - end of helix Processing helix chain 'B' and resid 1219 through 1237 Processing helix chain 'B' and resid 1240 through 1256 removed outlier: 3.589A pdb=" N GLN B1244 " --> pdb=" O ASN B1240 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B1246 " --> pdb=" O SER B1242 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B1247 " --> pdb=" O LEU B1243 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN B1248 " --> pdb=" O GLN B1244 " (cutoff:3.500A) Processing helix chain 'B' and resid 1261 through 1278 removed outlier: 3.559A pdb=" N GLY B1278 " --> pdb=" O LEU B1274 " (cutoff:3.500A) Processing helix chain 'B' and resid 1286 through 1292 removed outlier: 3.778A pdb=" N SER B1290 " --> pdb=" O LEU B1287 " (cutoff:3.500A) Processing helix chain 'B' and resid 1572 through 1589 Processing helix chain 'B' and resid 1593 through 1609 Processing helix chain 'B' and resid 1612 through 1622 Processing helix chain 'B' and resid 1625 through 1647 Processing helix chain 'B' and resid 1668 through 1678 Processing helix chain 'B' and resid 1688 through 1701 Processing helix chain 'B' and resid 1749 through 1770 removed outlier: 3.965A pdb=" N SER B1769 " --> pdb=" O LYS B1765 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N CYS B1770 " --> pdb=" O GLU B1766 " (cutoff:3.500A) Processing helix chain 'B' and resid 1772 through 1798 removed outlier: 3.517A pdb=" N GLU B1795 " --> pdb=" O ILE B1791 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B1798 " --> pdb=" O LEU B1794 " (cutoff:3.500A) Processing helix chain 'B' and resid 1799 through 1806 removed outlier: 3.504A pdb=" N GLY B1804 " --> pdb=" O CYS B1801 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1828 removed outlier: 4.261A pdb=" N GLU B1824 " --> pdb=" O SER B1820 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU B1825 " --> pdb=" O ARG B1821 " (cutoff:3.500A) Processing helix chain 'B' and resid 1835 through 1845 removed outlier: 4.007A pdb=" N GLY B1845 " --> pdb=" O ILE B1841 " (cutoff:3.500A) Processing helix chain 'B' and resid 1850 through 1862 Processing helix chain 'B' and resid 1865 through 1881 removed outlier: 3.669A pdb=" N ALA B1869 " --> pdb=" O GLN B1865 " (cutoff:3.500A) Processing helix chain 'B' and resid 1898 through 1902 removed outlier: 3.711A pdb=" N LYS B1901 " --> pdb=" O ASP B1898 " (cutoff:3.500A) Processing helix chain 'B' and resid 1903 through 1911 Proline residue: B1908 - end of helix removed outlier: 3.693A pdb=" N GLN B1911 " --> pdb=" O PRO B1908 " (cutoff:3.500A) Processing helix chain 'B' and resid 1920 through 1933 removed outlier: 3.634A pdb=" N LEU B1924 " --> pdb=" O SER B1920 " (cutoff:3.500A) Processing helix chain 'B' and resid 1958 through 1972 removed outlier: 3.923A pdb=" N GLU B1962 " --> pdb=" O LEU B1958 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ALA B1967 " --> pdb=" O GLU B1963 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASN B1968 " --> pdb=" O GLN B1964 " (cutoff:3.500A) Processing helix chain 'B' and resid 1984 through 1995 removed outlier: 3.601A pdb=" N VAL B1988 " --> pdb=" O ARG B1984 " (cutoff:3.500A) Processing helix chain 'B' and resid 2011 through 2017 Processing helix chain 'B' and resid 2044 through 2053 removed outlier: 3.788A pdb=" N LYS B2048 " --> pdb=" O GLY B2044 " (cutoff:3.500A) Processing helix chain 'B' and resid 2065 through 2084 removed outlier: 3.977A pdb=" N GLY B2084 " --> pdb=" O TRP B2080 " (cutoff:3.500A) Processing helix chain 'B' and resid 2088 through 2097 removed outlier: 3.754A pdb=" N TYR B2092 " --> pdb=" O PRO B2088 " (cutoff:3.500A) Processing helix chain 'B' and resid 2102 through 2107 Processing sheet with id=AA1, first strand: chain 'B' and resid 1737 through 1742 removed outlier: 4.389A pdb=" N THR B1724 " --> pdb=" O ALA B1714 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N THR B1707 " --> pdb=" O VAL B1892 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B1894 " --> pdb=" O THR B1707 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N CYS B1709 " --> pdb=" O VAL B1894 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 1976 through 1979 removed outlier: 6.167A pdb=" N THR B1948 " --> pdb=" O ARG B1976 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N VAL B1978 " --> pdb=" O THR B1948 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR B1950 " --> pdb=" O VAL B1978 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE B1949 " --> pdb=" O ILE B1999 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ALA B2001 " --> pdb=" O PHE B1949 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B1951 " --> pdb=" O ALA B2001 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR B1998 " --> pdb=" O LEU B2025 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA B2024 " --> pdb=" O LEU B2058 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ASN B2060 " --> pdb=" O ALA B2024 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N LEU B2026 " --> pdb=" O ASN B2060 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2709 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: 2.35 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4176 1.34 - 1.46: 2124 1.46 - 1.58: 6314 1.58 - 1.70: 0 1.70 - 1.81: 77 Bond restraints: 12691 Sorted by residual: bond pdb=" N VAL B 427 " pdb=" CA VAL B 427 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.19e-02 7.06e+03 1.02e+01 bond pdb=" N HIS B 470 " pdb=" CA HIS B 470 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.10e-02 8.26e+03 8.74e+00 bond pdb=" N VAL B2093 " pdb=" CA VAL B2093 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.66e+00 bond pdb=" N VAL B1246 " pdb=" CA VAL B1246 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.63e+00 bond pdb=" N VAL B 434 " pdb=" CA VAL B 434 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.61e+00 ... (remaining 12686 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 16199 1.92 - 3.84: 993 3.84 - 5.76: 80 5.76 - 7.67: 8 7.67 - 9.59: 6 Bond angle restraints: 17286 Sorted by residual: angle pdb=" N TYR B 730 " pdb=" CA TYR B 730 " pdb=" C TYR B 730 " ideal model delta sigma weight residual 114.31 106.28 8.03 1.29e+00 6.01e-01 3.87e+01 angle pdb=" CA ASP B 410 " pdb=" CB ASP B 410 " pdb=" CG ASP B 410 " ideal model delta sigma weight residual 112.60 117.86 -5.26 1.00e+00 1.00e+00 2.77e+01 angle pdb=" C ARG B 133 " pdb=" CA ARG B 133 " pdb=" CB ARG B 133 " ideal model delta sigma weight residual 116.54 111.02 5.52 1.15e+00 7.56e-01 2.30e+01 angle pdb=" C SER B 132 " pdb=" CA SER B 132 " pdb=" CB SER B 132 " ideal model delta sigma weight residual 116.54 111.54 5.00 1.15e+00 7.56e-01 1.89e+01 angle pdb=" N THR B 849 " pdb=" CA THR B 849 " pdb=" C THR B 849 " ideal model delta sigma weight residual 113.38 108.16 5.22 1.23e+00 6.61e-01 1.80e+01 ... (remaining 17281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 6991 17.58 - 35.16: 509 35.16 - 52.75: 111 52.75 - 70.33: 70 70.33 - 87.91: 5 Dihedral angle restraints: 7686 sinusoidal: 2762 harmonic: 4924 Sorted by residual: dihedral pdb=" CB CYS B 637 " pdb=" SG CYS B 637 " pdb=" SG CYS B 687 " pdb=" CB CYS B 687 " ideal model delta sinusoidal sigma weight residual -86.00 -154.31 68.31 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CA VAL B 187 " pdb=" C VAL B 187 " pdb=" N PRO B 188 " pdb=" CA PRO B 188 " ideal model delta harmonic sigma weight residual 180.00 150.36 29.64 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA PHE B 735 " pdb=" C PHE B 735 " pdb=" N ASN B 736 " pdb=" CA ASN B 736 " ideal model delta harmonic sigma weight residual 180.00 -160.28 -19.72 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 7683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1478 0.045 - 0.089: 359 0.089 - 0.134: 156 0.134 - 0.179: 46 0.179 - 0.224: 10 Chirality restraints: 2049 Sorted by residual: chirality pdb=" CA TYR B 730 " pdb=" N TYR B 730 " pdb=" C TYR B 730 " pdb=" CB TYR B 730 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA VAL B1938 " pdb=" N VAL B1938 " pdb=" C VAL B1938 " pdb=" CB VAL B1938 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA VAL B1885 " pdb=" N VAL B1885 " pdb=" C VAL B1885 " pdb=" CB VAL B1885 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2046 not shown) Planarity restraints: 2231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 378 " 0.276 9.50e-02 1.11e+02 1.24e-01 9.42e+00 pdb=" NE ARG B 378 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 378 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 378 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 378 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B1295 " 0.052 5.00e-02 4.00e+02 7.63e-02 9.31e+00 pdb=" N PRO B1296 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO B1296 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B1296 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 334 " 0.253 9.50e-02 1.11e+02 1.13e-01 7.88e+00 pdb=" NE ARG B 334 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 334 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 334 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 334 " 0.008 2.00e-02 2.50e+03 ... (remaining 2228 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1851 2.76 - 3.30: 12514 3.30 - 3.83: 20650 3.83 - 4.36: 24095 4.36 - 4.90: 40621 Nonbonded interactions: 99731 Sorted by model distance: nonbonded pdb=" O SER B 330 " pdb=" OG SER B 330 " model vdw 2.225 3.040 nonbonded pdb=" O GLU B 141 " pdb=" N GLY B 146 " model vdw 2.256 3.120 nonbonded pdb=" N GLU B 448 " pdb=" OE1 GLU B 448 " model vdw 2.275 3.120 nonbonded pdb=" OE2 GLU B 936 " pdb=" OG1 THR B1634 " model vdw 2.297 3.040 nonbonded pdb=" O ALA B 421 " pdb=" OG1 THR B 424 " model vdw 2.347 3.040 ... (remaining 99726 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 4.410 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.930 Find NCS groups from input model: 0.040 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:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 25.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 : 0.007 0.077 12696 Z= 0.473 Angle : 0.895 9.592 17291 Z= 0.628 Chirality : 0.052 0.224 2049 Planarity : 0.007 0.124 2231 Dihedral : 14.611 87.908 4483 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.73 % Allowed : 13.95 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.39 (0.20), residues: 1678 helix: 1.82 (0.15), residues: 1162 sheet: 1.61 (0.84), residues: 48 loop : -1.50 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 558 TYR 0.020 0.002 TYR B 459 PHE 0.017 0.002 PHE B 735 TRP 0.017 0.002 TRP B 683 HIS 0.006 0.001 HIS B1890 Details of bonding type rmsd covalent geometry : bond 0.00681 (12691) covalent geometry : angle 0.89465 (17286) SS BOND : bond 0.00497 ( 1) SS BOND : angle 0.66648 ( 2) hydrogen bonds : bond 0.19232 ( 918) hydrogen bonds : angle 5.71200 ( 2709) metal coordination : bond 0.00461 ( 4) metal coordination : angle 2.28200 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 205 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 LEU cc_start: 0.8987 (mt) cc_final: 0.8619 (mp) REVERT: B 364 PHE cc_start: 0.8619 (t80) cc_final: 0.8333 (t80) REVERT: B 700 ASP cc_start: 0.7993 (t70) cc_final: 0.7718 (t70) REVERT: B 1149 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8750 (p) REVERT: B 1836 ARG cc_start: 0.7931 (mtt-85) cc_final: 0.7300 (mtt-85) outliers start: 9 outliers final: 4 residues processed: 210 average time/residue: 0.5716 time to fit residues: 130.1871 Evaluate side-chains 179 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 174 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1149 SER Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1244 GLN Chi-restraints excluded: chain B residue 1713 LEU Chi-restraints excluded: chain B residue 1801 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 GLN B 341 GLN B 399 GLN B 644 GLN B 672 GLN B 749 GLN B 821 GLN B1203 GLN B1286 GLN B1631 GLN B1723 ASN B1761 GLN B1823 GLN B1827 GLN B1955 HIS B1964 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.073860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.053136 restraints weight = 29999.240| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 1.76 r_work: 0.2618 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12696 Z= 0.184 Angle : 0.629 10.160 17291 Z= 0.324 Chirality : 0.038 0.148 2049 Planarity : 0.005 0.049 2231 Dihedral : 5.087 87.149 1803 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.16 % Allowed : 15.90 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.63 (0.20), residues: 1678 helix: 1.91 (0.14), residues: 1193 sheet: 1.39 (0.81), residues: 48 loop : -1.33 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 558 TYR 0.031 0.002 TYR B 459 PHE 0.029 0.002 PHE B 393 TRP 0.016 0.002 TRP B 683 HIS 0.007 0.001 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00401 (12691) covalent geometry : angle 0.62832 (17286) SS BOND : bond 0.00449 ( 1) SS BOND : angle 0.29858 ( 2) hydrogen bonds : bond 0.06845 ( 918) hydrogen bonds : angle 4.48477 ( 2709) metal coordination : bond 0.00343 ( 4) metal coordination : angle 1.37982 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 358 ASP cc_start: 0.7849 (m-30) cc_final: 0.7621 (m-30) REVERT: B 364 PHE cc_start: 0.8846 (t80) cc_final: 0.8645 (t80) REVERT: B 380 ASP cc_start: 0.7329 (t0) cc_final: 0.7089 (t0) REVERT: B 399 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8548 (tm-30) REVERT: B 455 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8659 (mtm) REVERT: B 530 TRP cc_start: 0.8979 (t60) cc_final: 0.8678 (t60) REVERT: B 700 ASP cc_start: 0.8858 (t70) cc_final: 0.8511 (t70) REVERT: B 1046 LEU cc_start: 0.8507 (tp) cc_final: 0.8209 (tt) REVERT: B 1836 ARG cc_start: 0.8698 (mtt-85) cc_final: 0.8185 (mtt-85) outliers start: 39 outliers final: 13 residues processed: 205 average time/residue: 0.6282 time to fit residues: 139.6311 Evaluate side-chains 196 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain B residue 1209 LYS Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1574 LEU Chi-restraints excluded: chain B residue 1713 LEU Chi-restraints excluded: chain B residue 1850 THR Chi-restraints excluded: chain B residue 1888 ASN Chi-restraints excluded: chain B residue 2045 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 0.5980 chunk 164 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 96 optimal weight: 0.5980 chunk 120 optimal weight: 0.9980 chunk 154 optimal weight: 0.2980 chunk 12 optimal weight: 0.0070 chunk 27 optimal weight: 0.9980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN B 821 GLN B1955 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.074725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.053961 restraints weight = 30190.886| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 1.78 r_work: 0.2642 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12696 Z= 0.150 Angle : 0.578 8.692 17291 Z= 0.293 Chirality : 0.037 0.151 2049 Planarity : 0.005 0.057 2231 Dihedral : 4.486 57.527 1798 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.08 % Allowed : 17.60 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1678 helix: 2.06 (0.15), residues: 1191 sheet: 1.36 (0.80), residues: 48 loop : -1.26 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 378 TYR 0.015 0.002 TYR B 409 PHE 0.040 0.002 PHE B 393 TRP 0.014 0.001 TRP B 683 HIS 0.005 0.001 HIS B1630 Details of bonding type rmsd covalent geometry : bond 0.00321 (12691) covalent geometry : angle 0.57758 (17286) SS BOND : bond 0.00244 ( 1) SS BOND : angle 2.09207 ( 2) hydrogen bonds : bond 0.05761 ( 918) hydrogen bonds : angle 4.24163 ( 2709) metal coordination : bond 0.00246 ( 4) metal coordination : angle 1.19399 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 313 LYS cc_start: 0.8429 (tppp) cc_final: 0.8134 (mmtp) REVERT: B 364 PHE cc_start: 0.8776 (t80) cc_final: 0.8531 (t80) REVERT: B 380 ASP cc_start: 0.7464 (t0) cc_final: 0.7094 (t0) REVERT: B 459 TYR cc_start: 0.8535 (m-80) cc_final: 0.8213 (m-80) REVERT: B 530 TRP cc_start: 0.8964 (t60) cc_final: 0.8704 (t60) REVERT: B 700 ASP cc_start: 0.8897 (t70) cc_final: 0.8501 (t70) REVERT: B 1219 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8352 (mp) REVERT: B 1836 ARG cc_start: 0.8678 (mtt-85) cc_final: 0.8193 (mtt-85) outliers start: 38 outliers final: 18 residues processed: 212 average time/residue: 0.6001 time to fit residues: 138.1200 Evaluate side-chains 196 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 376 GLN Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 1061 CYS Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1244 GLN Chi-restraints excluded: chain B residue 1248 GLN Chi-restraints excluded: chain B residue 1574 LEU Chi-restraints excluded: chain B residue 1713 LEU Chi-restraints excluded: chain B residue 1773 LYS Chi-restraints excluded: chain B residue 1811 GLU Chi-restraints excluded: chain B residue 1850 THR Chi-restraints excluded: chain B residue 2045 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 0.5980 chunk 146 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 27 optimal weight: 0.0980 chunk 145 optimal weight: 1.9990 chunk 126 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 167 optimal weight: 0.0170 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 GLN B1203 GLN B1955 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.075117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.054358 restraints weight = 30191.878| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 1.78 r_work: 0.2652 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12696 Z= 0.138 Angle : 0.578 10.329 17291 Z= 0.286 Chirality : 0.036 0.163 2049 Planarity : 0.005 0.060 2231 Dihedral : 4.399 58.358 1798 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.76 % Allowed : 18.00 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.95 (0.20), residues: 1678 helix: 2.14 (0.14), residues: 1191 sheet: 1.36 (0.79), residues: 48 loop : -1.17 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 702 TYR 0.018 0.002 TYR B 459 PHE 0.038 0.002 PHE B 393 TRP 0.013 0.001 TRP B 683 HIS 0.004 0.001 HIS B1630 Details of bonding type rmsd covalent geometry : bond 0.00295 (12691) covalent geometry : angle 0.57745 (17286) SS BOND : bond 0.00419 ( 1) SS BOND : angle 0.77528 ( 2) hydrogen bonds : bond 0.05182 ( 918) hydrogen bonds : angle 4.05110 ( 2709) metal coordination : bond 0.00218 ( 4) metal coordination : angle 1.13428 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 313 LYS cc_start: 0.8426 (tppp) cc_final: 0.8140 (mmtp) REVERT: B 380 ASP cc_start: 0.7446 (t0) cc_final: 0.7060 (t0) REVERT: B 399 GLN cc_start: 0.8948 (tp40) cc_final: 0.8384 (tm-30) REVERT: B 700 ASP cc_start: 0.8899 (t70) cc_final: 0.8490 (t70) REVERT: B 728 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7533 (m-80) REVERT: B 1812 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.7465 (mm-30) REVERT: B 1836 ARG cc_start: 0.8665 (mtt-85) cc_final: 0.8170 (mtt-85) outliers start: 34 outliers final: 21 residues processed: 204 average time/residue: 0.6153 time to fit residues: 136.1610 Evaluate side-chains 198 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain B residue 728 PHE Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 1061 CYS Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1248 GLN Chi-restraints excluded: chain B residue 1288 PHE Chi-restraints excluded: chain B residue 1574 LEU Chi-restraints excluded: chain B residue 1713 LEU Chi-restraints excluded: chain B residue 1715 THR Chi-restraints excluded: chain B residue 1773 LYS Chi-restraints excluded: chain B residue 1811 GLU Chi-restraints excluded: chain B residue 1812 GLU Chi-restraints excluded: chain B residue 1850 THR Chi-restraints excluded: chain B residue 1888 ASN Chi-restraints excluded: chain B residue 2045 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 148 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 133 optimal weight: 0.0970 chunk 41 optimal weight: 0.4980 chunk 95 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 chunk 79 optimal weight: 0.0070 chunk 123 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1203 GLN B1823 GLN B1955 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.075022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.054091 restraints weight = 30351.450| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 1.84 r_work: 0.2642 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12696 Z= 0.139 Angle : 0.588 12.118 17291 Z= 0.290 Chirality : 0.036 0.148 2049 Planarity : 0.005 0.078 2231 Dihedral : 4.350 58.449 1798 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.84 % Allowed : 19.06 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 2.10 (0.20), residues: 1678 helix: 2.25 (0.15), residues: 1192 sheet: 1.32 (0.79), residues: 48 loop : -1.10 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 664 TYR 0.020 0.002 TYR B 337 PHE 0.046 0.002 PHE B 393 TRP 0.013 0.001 TRP B 683 HIS 0.006 0.001 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00308 (12691) covalent geometry : angle 0.58815 (17286) SS BOND : bond 0.00415 ( 1) SS BOND : angle 0.61313 ( 2) hydrogen bonds : bond 0.05044 ( 918) hydrogen bonds : angle 3.97156 ( 2709) metal coordination : bond 0.00228 ( 4) metal coordination : angle 1.15328 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 380 ASP cc_start: 0.7581 (t0) cc_final: 0.7271 (t0) REVERT: B 399 GLN cc_start: 0.8941 (tp40) cc_final: 0.8457 (tm-30) REVERT: B 465 TYR cc_start: 0.8447 (t80) cc_final: 0.8240 (t80) REVERT: B 700 ASP cc_start: 0.8908 (t70) cc_final: 0.8472 (t70) REVERT: B 728 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: B 1812 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.7471 (mm-30) REVERT: B 1836 ARG cc_start: 0.8661 (mtt-85) cc_final: 0.8154 (mtt-85) outliers start: 35 outliers final: 19 residues processed: 202 average time/residue: 0.5994 time to fit residues: 131.9219 Evaluate side-chains 195 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain B residue 728 PHE Chi-restraints excluded: chain B residue 950 ILE Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 1061 CYS Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1248 GLN Chi-restraints excluded: chain B residue 1713 LEU Chi-restraints excluded: chain B residue 1715 THR Chi-restraints excluded: chain B residue 1773 LYS Chi-restraints excluded: chain B residue 1811 GLU Chi-restraints excluded: chain B residue 1812 GLU Chi-restraints excluded: chain B residue 1850 THR Chi-restraints excluded: chain B residue 1888 ASN Chi-restraints excluded: chain B residue 2045 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 114 optimal weight: 0.3980 chunk 84 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 153 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 124 optimal weight: 0.0570 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 821 GLN B 997 HIS B1203 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.074659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.053662 restraints weight = 30317.660| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 1.84 r_work: 0.2628 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12696 Z= 0.148 Angle : 0.596 12.600 17291 Z= 0.295 Chirality : 0.036 0.146 2049 Planarity : 0.005 0.064 2231 Dihedral : 4.360 59.025 1798 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.92 % Allowed : 19.22 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 2.11 (0.20), residues: 1678 helix: 2.27 (0.14), residues: 1192 sheet: 1.29 (0.79), residues: 48 loop : -1.13 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 664 TYR 0.014 0.001 TYR B2092 PHE 0.045 0.002 PHE B 393 TRP 0.013 0.001 TRP B 683 HIS 0.006 0.001 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00334 (12691) covalent geometry : angle 0.59544 (17286) SS BOND : bond 0.00376 ( 1) SS BOND : angle 0.44546 ( 2) hydrogen bonds : bond 0.05128 ( 918) hydrogen bonds : angle 3.95156 ( 2709) metal coordination : bond 0.00265 ( 4) metal coordination : angle 1.11337 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 LEU cc_start: 0.8964 (tp) cc_final: 0.8757 (tt) REVERT: B 380 ASP cc_start: 0.7595 (t0) cc_final: 0.7190 (t0) REVERT: B 399 GLN cc_start: 0.8941 (tp40) cc_final: 0.8531 (tm-30) REVERT: B 530 TRP cc_start: 0.8915 (t60) cc_final: 0.8680 (t60) REVERT: B 664 ARG cc_start: 0.8463 (mtm110) cc_final: 0.8234 (ptp-110) REVERT: B 700 ASP cc_start: 0.8905 (t70) cc_final: 0.8465 (t70) REVERT: B 728 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: B 1812 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.7469 (mm-30) REVERT: B 1836 ARG cc_start: 0.8675 (mtt-85) cc_final: 0.8140 (mtt-85) REVERT: B 2095 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8111 (tt0) outliers start: 36 outliers final: 21 residues processed: 196 average time/residue: 0.6136 time to fit residues: 131.0543 Evaluate side-chains 194 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain B residue 728 PHE Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 950 ILE Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 1061 CYS Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1244 GLN Chi-restraints excluded: chain B residue 1248 GLN Chi-restraints excluded: chain B residue 1713 LEU Chi-restraints excluded: chain B residue 1715 THR Chi-restraints excluded: chain B residue 1773 LYS Chi-restraints excluded: chain B residue 1811 GLU Chi-restraints excluded: chain B residue 1812 GLU Chi-restraints excluded: chain B residue 1850 THR Chi-restraints excluded: chain B residue 2045 ILE Chi-restraints excluded: chain B residue 2095 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 86 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 115 optimal weight: 0.0870 chunk 138 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 821 GLN B1203 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.074207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.053243 restraints weight = 29990.809| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 1.83 r_work: 0.2616 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12696 Z= 0.156 Angle : 0.604 10.020 17291 Z= 0.301 Chirality : 0.037 0.146 2049 Planarity : 0.005 0.059 2231 Dihedral : 4.382 59.668 1798 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.84 % Allowed : 20.03 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 2.11 (0.20), residues: 1678 helix: 2.26 (0.14), residues: 1194 sheet: 1.23 (0.79), residues: 48 loop : -1.10 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 664 TYR 0.020 0.002 TYR B 459 PHE 0.041 0.002 PHE B 393 TRP 0.013 0.001 TRP B 683 HIS 0.007 0.001 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00354 (12691) covalent geometry : angle 0.60282 (17286) SS BOND : bond 0.00840 ( 1) SS BOND : angle 3.20316 ( 2) hydrogen bonds : bond 0.05249 ( 918) hydrogen bonds : angle 3.95942 ( 2709) metal coordination : bond 0.00387 ( 4) metal coordination : angle 1.08155 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 399 GLN cc_start: 0.8932 (tp40) cc_final: 0.8524 (tm-30) REVERT: B 700 ASP cc_start: 0.8917 (t70) cc_final: 0.8464 (t70) REVERT: B 728 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7527 (m-80) REVERT: B 1812 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.7464 (mm-30) REVERT: B 1836 ARG cc_start: 0.8684 (mtt-85) cc_final: 0.8137 (mtt-85) REVERT: B 2095 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8115 (tt0) outliers start: 35 outliers final: 19 residues processed: 193 average time/residue: 0.6072 time to fit residues: 127.4272 Evaluate side-chains 195 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain B residue 728 PHE Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 1061 CYS Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1232 LEU Chi-restraints excluded: chain B residue 1239 SER Chi-restraints excluded: chain B residue 1244 GLN Chi-restraints excluded: chain B residue 1248 GLN Chi-restraints excluded: chain B residue 1713 LEU Chi-restraints excluded: chain B residue 1773 LYS Chi-restraints excluded: chain B residue 1811 GLU Chi-restraints excluded: chain B residue 1812 GLU Chi-restraints excluded: chain B residue 1850 THR Chi-restraints excluded: chain B residue 1986 GLU Chi-restraints excluded: chain B residue 2045 ILE Chi-restraints excluded: chain B residue 2095 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 48 optimal weight: 0.8980 chunk 135 optimal weight: 0.5980 chunk 2 optimal weight: 10.0000 chunk 142 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 164 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 821 GLN ** B1203 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 = 0.3207 r_free = 0.3207 target = 0.073056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.051996 restraints weight = 29864.779| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 1.84 r_work: 0.2583 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12696 Z= 0.194 Angle : 0.666 13.575 17291 Z= 0.335 Chirality : 0.039 0.199 2049 Planarity : 0.005 0.067 2231 Dihedral : 4.476 59.907 1798 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.76 % Allowed : 20.84 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.98 (0.20), residues: 1678 helix: 2.17 (0.14), residues: 1191 sheet: 1.23 (0.79), residues: 48 loop : -1.16 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 664 TYR 0.036 0.002 TYR B 459 PHE 0.044 0.002 PHE B 393 TRP 0.014 0.002 TRP B 683 HIS 0.007 0.001 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00456 (12691) covalent geometry : angle 0.66517 (17286) SS BOND : bond 0.00920 ( 1) SS BOND : angle 3.42688 ( 2) hydrogen bonds : bond 0.05825 ( 918) hydrogen bonds : angle 4.07023 ( 2709) metal coordination : bond 0.00747 ( 4) metal coordination : angle 1.15367 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 324 LYS cc_start: 0.8766 (pptt) cc_final: 0.8523 (pttt) REVERT: B 399 GLN cc_start: 0.8932 (tp40) cc_final: 0.8509 (tm-30) REVERT: B 700 ASP cc_start: 0.8909 (t70) cc_final: 0.8440 (t70) REVERT: B 833 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: B 1812 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.7010 (mt-10) REVERT: B 2095 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8136 (tt0) outliers start: 34 outliers final: 18 residues processed: 193 average time/residue: 0.5993 time to fit residues: 125.7046 Evaluate side-chains 189 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 833 GLN Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 1061 CYS Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1239 SER Chi-restraints excluded: chain B residue 1244 GLN Chi-restraints excluded: chain B residue 1248 GLN Chi-restraints excluded: chain B residue 1713 LEU Chi-restraints excluded: chain B residue 1811 GLU Chi-restraints excluded: chain B residue 1812 GLU Chi-restraints excluded: chain B residue 1850 THR Chi-restraints excluded: chain B residue 1986 GLU Chi-restraints excluded: chain B residue 2045 ILE Chi-restraints excluded: chain B residue 2095 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 GLN B 821 GLN B1203 GLN B1823 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.073503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.052450 restraints weight = 30093.251| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 1.84 r_work: 0.2597 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2495 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12696 Z= 0.173 Angle : 0.663 14.307 17291 Z= 0.332 Chirality : 0.039 0.267 2049 Planarity : 0.005 0.101 2231 Dihedral : 4.479 59.870 1798 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.11 % Allowed : 21.65 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.99 (0.20), residues: 1678 helix: 2.18 (0.15), residues: 1192 sheet: 1.22 (0.79), residues: 48 loop : -1.17 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 664 TYR 0.028 0.002 TYR B 459 PHE 0.046 0.002 PHE B 393 TRP 0.015 0.002 TRP B 683 HIS 0.006 0.001 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00402 (12691) covalent geometry : angle 0.66227 (17286) SS BOND : bond 0.00664 ( 1) SS BOND : angle 2.47804 ( 2) hydrogen bonds : bond 0.05549 ( 918) hydrogen bonds : angle 4.04964 ( 2709) metal coordination : bond 0.00510 ( 4) metal coordination : angle 0.76837 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 324 LYS cc_start: 0.8757 (pptt) cc_final: 0.8532 (pttt) REVERT: B 358 ASP cc_start: 0.7709 (m-30) cc_final: 0.7484 (m-30) REVERT: B 573 LEU cc_start: 0.9382 (tp) cc_final: 0.9118 (tm) REVERT: B 664 ARG cc_start: 0.8492 (mtm110) cc_final: 0.8264 (ptp-110) REVERT: B 700 ASP cc_start: 0.8919 (t70) cc_final: 0.8449 (t70) REVERT: B 1181 LEU cc_start: 0.8339 (mp) cc_final: 0.7868 (mt) REVERT: B 1219 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8361 (mt) REVERT: B 1812 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.7037 (mt-10) REVERT: B 1836 ARG cc_start: 0.8690 (mtt-85) cc_final: 0.8230 (mtt-85) outliers start: 26 outliers final: 15 residues processed: 185 average time/residue: 0.6142 time to fit residues: 123.3588 Evaluate side-chains 183 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 1061 CYS Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1239 SER Chi-restraints excluded: chain B residue 1248 GLN Chi-restraints excluded: chain B residue 1642 LYS Chi-restraints excluded: chain B residue 1713 LEU Chi-restraints excluded: chain B residue 1811 GLU Chi-restraints excluded: chain B residue 1812 GLU Chi-restraints excluded: chain B residue 1850 THR Chi-restraints excluded: chain B residue 1986 GLU Chi-restraints excluded: chain B residue 2045 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 59 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 110 optimal weight: 0.0670 chunk 143 optimal weight: 0.0970 chunk 17 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN B 590 GLN B 762 GLN B 821 GLN B1203 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.074426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.053389 restraints weight = 30234.718| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 1.86 r_work: 0.2621 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12696 Z= 0.150 Angle : 0.636 15.527 17291 Z= 0.321 Chirality : 0.037 0.286 2049 Planarity : 0.005 0.071 2231 Dihedral : 4.383 59.550 1798 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.70 % Allowed : 22.06 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 2.13 (0.21), residues: 1678 helix: 2.29 (0.15), residues: 1194 sheet: 1.20 (0.79), residues: 48 loop : -1.14 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 664 TYR 0.016 0.002 TYR B 459 PHE 0.051 0.002 PHE B 393 TRP 0.014 0.001 TRP B 683 HIS 0.004 0.001 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00339 (12691) covalent geometry : angle 0.63570 (17286) SS BOND : bond 0.00536 ( 1) SS BOND : angle 2.16733 ( 2) hydrogen bonds : bond 0.05065 ( 918) hydrogen bonds : angle 3.96904 ( 2709) metal coordination : bond 0.00203 ( 4) metal coordination : angle 0.57760 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 358 ASP cc_start: 0.7644 (m-30) cc_final: 0.7413 (m-30) REVERT: B 399 GLN cc_start: 0.8892 (tm130) cc_final: 0.8407 (tm-30) REVERT: B 459 TYR cc_start: 0.8322 (m-10) cc_final: 0.8016 (m-10) REVERT: B 573 LEU cc_start: 0.9394 (tp) cc_final: 0.9127 (tm) REVERT: B 664 ARG cc_start: 0.8460 (mtm110) cc_final: 0.8230 (ptp-110) REVERT: B 700 ASP cc_start: 0.8902 (t70) cc_final: 0.8452 (t70) REVERT: B 728 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7467 (m-80) REVERT: B 1181 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7781 (mt) REVERT: B 1219 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8328 (mt) REVERT: B 1812 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.7476 (mm-30) REVERT: B 1836 ARG cc_start: 0.8671 (mtt-85) cc_final: 0.8227 (mtt-85) outliers start: 21 outliers final: 15 residues processed: 189 average time/residue: 0.6314 time to fit residues: 129.5971 Evaluate side-chains 189 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain B residue 728 PHE Chi-restraints excluded: chain B residue 950 ILE Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1239 SER Chi-restraints excluded: chain B residue 1248 GLN Chi-restraints excluded: chain B residue 1642 LYS Chi-restraints excluded: chain B residue 1713 LEU Chi-restraints excluded: chain B residue 1811 GLU Chi-restraints excluded: chain B residue 1812 GLU Chi-restraints excluded: chain B residue 1850 THR Chi-restraints excluded: chain B residue 2045 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 83 optimal weight: 0.0030 chunk 47 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 103 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 148 optimal weight: 0.0570 overall best weight: 0.3708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN B 736 ASN B 762 GLN B 821 GLN B1203 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.075107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.054142 restraints weight = 30120.561| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 1.85 r_work: 0.2641 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12696 Z= 0.141 Angle : 0.643 15.277 17291 Z= 0.322 Chirality : 0.037 0.241 2049 Planarity : 0.005 0.079 2231 Dihedral : 4.307 59.205 1798 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.95 % Allowed : 22.06 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 2.24 (0.21), residues: 1678 helix: 2.38 (0.15), residues: 1196 sheet: 1.19 (0.78), residues: 48 loop : -1.12 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 664 TYR 0.014 0.001 TYR B2092 PHE 0.050 0.002 PHE B 393 TRP 0.014 0.001 TRP B 683 HIS 0.005 0.001 HIS B 402 Details of bonding type rmsd covalent geometry : bond 0.00315 (12691) covalent geometry : angle 0.64318 (17286) SS BOND : bond 0.00420 ( 1) SS BOND : angle 1.97961 ( 2) hydrogen bonds : bond 0.04751 ( 918) hydrogen bonds : angle 3.90771 ( 2709) metal coordination : bond 0.00103 ( 4) metal coordination : angle 0.60892 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5284.42 seconds wall clock time: 90 minutes 40.88 seconds (5440.88 seconds total)