Starting phenix.real_space_refine on Sat Jul 4 23:02:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zpj_14855/07_2026/7zpj_14855.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zpj_14855/07_2026/7zpj_14855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zpj_14855/07_2026/7zpj_14855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zpj_14855/07_2026/7zpj_14855.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zpj_14855/07_2026/7zpj_14855.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zpj_14855/07_2026/7zpj_14855.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zpj_14855/07_2026/7zpj_14855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zpj_14855/07_2026/7zpj_14855.cif" } resolution = 3.81 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= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 55 5.49 5 S 63 5.16 5 C 7428 2.51 5 N 2043 2.21 5 O 2382 1.98 5 H 11508 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23479 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 20612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1280, 20612 Classifications: {'peptide': 1280} Link IDs: {'PTRANS': 76, 'TRANS': 1203} Chain breaks: 9 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1763 Classifications: {'RNA': 55} Modifications used: {'3*END': 1, 'rna3p_pur': 28, 'rna3p_pyr': 27} Link IDs: {'rna3p': 54} Chain breaks: 1 Chain: "D" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1104 Classifications: {'peptide': 75} Link IDs: {'PCIS': 1, 'TRANS': 73} Time building chain proxies: 3.83, per 1000 atoms: 0.16 Number of scatterers: 23479 At special positions: 0 Unit cell: (98.53, 122.745, 163.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 55 15.00 O 2382 8.00 N 2043 7.00 C 7428 6.00 H 11508 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 431.6 milliseconds 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 10 sheets defined 53.6% alpha, 12.4% beta 17 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 4.03 Creating SS restraints... Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.527A pdb=" N LYS A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 4.147A pdb=" N GLN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 162 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 184 through 196 removed outlier: 4.292A pdb=" N GLU A 188 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 231 removed outlier: 5.037A pdb=" N GLU A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 265 through 284 Processing helix chain 'A' and resid 294 through 314 Processing helix chain 'A' and resid 314 through 334 removed outlier: 3.855A pdb=" N LYS A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 361 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.653A pdb=" N LYS A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 468 Processing helix chain 'A' and resid 498 through 510 removed outlier: 3.661A pdb=" N GLU A 502 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 542 through 551 Processing helix chain 'A' and resid 565 through 592 removed outlier: 3.981A pdb=" N LYS A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER A 571 " --> pdb=" O ASP A 567 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU A 574 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 641 removed outlier: 4.317A pdb=" N GLY A 632 " --> pdb=" O ASN A 628 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 641 " --> pdb=" O TYR A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 706 removed outlier: 3.565A pdb=" N LYS A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 859 Processing helix chain 'A' and resid 893 through 902 Processing helix chain 'A' and resid 967 through 976 Processing helix chain 'A' and resid 1044 through 1053 removed outlier: 4.085A pdb=" N CYS A1053 " --> pdb=" O ARG A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1076 Processing helix chain 'A' and resid 1293 through 1302 Processing helix chain 'A' and resid 1303 through 1307 Processing helix chain 'A' and resid 1313 through 1335 Processing helix chain 'A' and resid 1339 through 1351 Processing helix chain 'A' and resid 1352 through 1363 Processing helix chain 'A' and resid 1364 through 1368 Processing helix chain 'A' and resid 1552 through 1583 removed outlier: 3.659A pdb=" N GLY A1571 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLU A1572 " --> pdb=" O THR A1568 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N ARG A1573 " --> pdb=" O SER A1569 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA A1574 " --> pdb=" O CYS A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1648 through 1657 Processing helix chain 'A' and resid 1660 through 1668 removed outlier: 3.728A pdb=" N LYS A1666 " --> pdb=" O THR A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1674 through 1682 removed outlier: 3.787A pdb=" N LEU A1678 " --> pdb=" O LYS A1674 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1716 removed outlier: 3.616A pdb=" N PHE A1700 " --> pdb=" O GLN A1696 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A1701 " --> pdb=" O ARG A1697 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A1704 " --> pdb=" O PHE A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1735 Processing helix chain 'A' and resid 1735 through 1746 Processing helix chain 'A' and resid 1747 through 1752 removed outlier: 4.020A pdb=" N TYR A1751 " --> pdb=" O ASP A1747 " (cutoff:3.500A) Processing helix chain 'A' and resid 1756 through 1773 removed outlier: 3.590A pdb=" N LYS A1768 " --> pdb=" O ASP A1764 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS A1773 " --> pdb=" O PHE A1769 " (cutoff:3.500A) Processing helix chain 'A' and resid 1799 through 1817 removed outlier: 3.868A pdb=" N GLY A1803 " --> pdb=" O PRO A1799 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1842 removed outlier: 3.509A pdb=" N VAL A1824 " --> pdb=" O SER A1820 " (cutoff:3.500A) Proline residue: A1830 - end of helix Proline residue: A1834 - end of helix removed outlier: 3.933A pdb=" N LYS A1838 " --> pdb=" O PRO A1834 " (cutoff:3.500A) Processing helix chain 'A' and resid 1846 through 1855 Processing helix chain 'A' and resid 1890 through 1910 Processing helix chain 'D' and resid 292 through 304 Processing helix chain 'D' and resid 342 through 364 Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.942A pdb=" N THR A 151 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR A 96 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N MET A 150 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N PHE A 98 " --> pdb=" O MET A 150 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ARG A 95 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU A 171 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 97 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 173 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP A 175 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR A 60 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N THR A 206 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL A 62 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE A 61 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 251 through 256 removed outlier: 6.166A pdb=" N CYS A 251 " --> pdb=" O TYR A 560 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET A 562 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 253 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ALA A 564 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL A 255 " --> pdb=" O ALA A 564 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A 445 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASN A 477 " --> pdb=" O ILE A 517 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 652 through 656 Processing sheet with id=AA4, first strand: chain 'A' and resid 746 through 750 Processing sheet with id=AA5, first strand: chain 'A' and resid 816 through 820 removed outlier: 3.800A pdb=" N PHE A 816 " --> pdb=" O ILE A 827 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N GLU A 824 " --> pdb=" O THR A 778 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A 832 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU A 770 " --> pdb=" O LYS A 832 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N SER A 834 " --> pdb=" O CYS A 768 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N CYS A 768 " --> pdb=" O SER A 834 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N PHE A 802 " --> pdb=" O ILE A 773 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR A 889 " --> pdb=" O VAL A 884 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 865 through 867 Processing sheet with id=AA7, first strand: chain 'A' and resid 987 through 992 removed outlier: 6.176A pdb=" N ASP A 991 " --> pdb=" O VAL A 947 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL A 947 " --> pdb=" O ASP A 991 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1859 through 1861 Processing sheet with id=AA9, first strand: chain 'A' and resid 1859 through 1861 Processing sheet with id=AB1, first strand: chain 'D' and resid 308 through 312 581 hydrogen bonds defined for protein. 1671 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 5.44 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 11467 1.02 - 1.22: 49 1.22 - 1.42: 5060 1.42 - 1.62: 7181 1.62 - 1.82: 85 Bond restraints: 23842 Sorted by residual: bond pdb=" NH1 ARG A 86 " pdb="HH12 ARG A 86 " ideal model delta sigma weight residual 0.860 0.819 0.041 2.00e-02 2.50e+03 4.11e+00 bond pdb=" NH1 ARG A 800 " pdb="HH12 ARG A 800 " ideal model delta sigma weight residual 0.860 0.826 0.034 2.00e-02 2.50e+03 2.89e+00 bond pdb=" NE2 GLN A 985 " pdb="HE22 GLN A 985 " ideal model delta sigma weight residual 0.860 0.828 0.032 2.00e-02 2.50e+03 2.59e+00 bond pdb=" C ILE A 773 " pdb=" N GLY A 774 " ideal model delta sigma weight residual 1.330 1.319 0.011 8.80e-03 1.29e+04 1.67e+00 bond pdb=" NH2 ARG A 640 " pdb="HH22 ARG A 640 " ideal model delta sigma weight residual 0.860 0.835 0.025 2.00e-02 2.50e+03 1.62e+00 ... (remaining 23837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.58: 43165 7.58 - 15.17: 6 15.17 - 22.75: 0 22.75 - 30.33: 2 30.33 - 37.91: 4 Bond angle restraints: 43177 Sorted by residual: angle pdb=" CB ALA A 464 " pdb=" CA ALA A 464 " pdb=" HA ALA A 464 " ideal model delta sigma weight residual 109.00 71.09 37.91 3.00e+00 1.11e-01 1.60e+02 angle pdb=" N ALA A 464 " pdb=" CA ALA A 464 " pdb=" HA ALA A 464 " ideal model delta sigma weight residual 110.00 75.34 34.66 3.00e+00 1.11e-01 1.34e+02 angle pdb=" O3' G B 26 " pdb=" C3' G B 26 " pdb=" H3' G B 26 " ideal model delta sigma weight residual 109.00 76.55 32.45 3.00e+00 1.11e-01 1.17e+02 angle pdb=" C ALA A 464 " pdb=" CA ALA A 464 " pdb=" HA ALA A 464 " ideal model delta sigma weight residual 109.00 77.57 31.43 3.00e+00 1.11e-01 1.10e+02 angle pdb=" C2' G B 26 " pdb=" C3' G B 26 " pdb=" H3' G B 26 " ideal model delta sigma weight residual 109.00 79.64 29.36 3.00e+00 1.11e-01 9.58e+01 ... (remaining 43172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 10826 35.91 - 71.81: 241 71.81 - 107.72: 14 107.72 - 143.63: 1 143.63 - 179.53: 9 Dihedral angle restraints: 11091 sinusoidal: 6437 harmonic: 4654 Sorted by residual: dihedral pdb=" O4' U B 27 " pdb=" C1' U B 27 " pdb=" N1 U B 27 " pdb=" C2 U B 27 " ideal model delta sinusoidal sigma weight residual 200.00 55.37 144.63 1 1.50e+01 4.44e-03 7.75e+01 dihedral pdb=" O4' U B 28 " pdb=" C1' U B 28 " pdb=" N1 U B 28 " pdb=" C2 U B 28 " ideal model delta sinusoidal sigma weight residual 200.00 60.31 139.69 1 1.50e+01 4.44e-03 7.52e+01 dihedral pdb=" CG TRP A 316 " pdb=" CD2 TRP A 316 " pdb=" CE3 TRP A 316 " pdb=" HE3 TRP A 316 " ideal model delta harmonic sigma weight residual 0.00 24.94 -24.94 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 11088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 1970 0.183 - 0.365: 12 0.365 - 0.548: 0 0.548 - 0.730: 0 0.730 - 0.913: 1 Chirality restraints: 1983 Sorted by residual: chirality pdb=" C3' G B 26 " pdb=" C4' G B 26 " pdb=" O3' G B 26 " pdb=" C2' G B 26 " both_signs ideal model delta sigma weight residual False -2.48 -1.56 -0.91 2.00e-01 2.50e+01 2.08e+01 chirality pdb=" CA ALA A 464 " pdb=" N ALA A 464 " pdb=" C ALA A 464 " pdb=" CB ALA A 464 " both_signs ideal model delta sigma weight residual False 2.48 2.18 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" P U B 28 " pdb=" OP1 U B 28 " pdb=" OP2 U B 28 " pdb=" O5' U B 28 " both_signs ideal model delta sigma weight residual True 2.41 -2.71 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 1980 not shown) Planarity restraints: 3263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 316 " 0.028 2.00e-02 2.50e+03 6.16e-02 1.52e+02 pdb=" CG TRP A 316 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 316 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 316 " -0.023 2.00e-02 2.50e+03 pdb=" NE1 TRP A 316 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TRP A 316 " -0.040 2.00e-02 2.50e+03 pdb=" CE3 TRP A 316 " 0.120 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 316 " -0.061 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 316 " -0.105 2.00e-02 2.50e+03 pdb=" CH2 TRP A 316 " -0.077 2.00e-02 2.50e+03 pdb=" HD1 TRP A 316 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 TRP A 316 " 0.046 2.00e-02 2.50e+03 pdb=" HE3 TRP A 316 " -0.057 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 316 " 0.063 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 316 " 0.054 2.00e-02 2.50e+03 pdb=" HH2 TRP A 316 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 86 " -0.268 9.50e-02 1.11e+02 1.16e-01 1.30e+02 pdb=" NE ARG A 86 " -0.081 2.00e-02 2.50e+03 pdb=" CZ ARG A 86 " 0.082 2.00e-02 2.50e+03 pdb=" NH1 ARG A 86 " 0.126 2.00e-02 2.50e+03 pdb=" NH2 ARG A 86 " 0.043 2.00e-02 2.50e+03 pdb="HH11 ARG A 86 " 0.011 2.00e-02 2.50e+03 pdb="HH12 ARG A 86 " -0.125 2.00e-02 2.50e+03 pdb="HH21 ARG A 86 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 86 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 187 " -0.421 9.50e-02 1.11e+02 1.51e-01 9.05e+01 pdb=" NE ARG A 187 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG A 187 " 0.053 2.00e-02 2.50e+03 pdb=" NH1 ARG A 187 " 0.077 2.00e-02 2.50e+03 pdb=" NH2 ARG A 187 " 0.080 2.00e-02 2.50e+03 pdb="HH11 ARG A 187 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 187 " -0.062 2.00e-02 2.50e+03 pdb="HH21 ARG A 187 " 0.003 2.00e-02 2.50e+03 pdb="HH22 ARG A 187 " -0.082 2.00e-02 2.50e+03 ... (remaining 3260 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1023 2.18 - 2.78: 46703 2.78 - 3.39: 65218 3.39 - 3.99: 81336 3.99 - 4.60: 127023 Nonbonded interactions: 321303 Sorted by model distance: nonbonded pdb="HH21 ARG A 935 " pdb=" O GLU A1036 " model vdw 1.574 2.450 nonbonded pdb=" HG1 THR A1867 " pdb=" OD1 ASP A1869 " model vdw 1.582 2.450 nonbonded pdb=" O LEU A1678 " pdb=" HG1 THR A1682 " model vdw 1.594 2.450 nonbonded pdb=" O GLU A 542 " pdb=" HG SER A 545 " model vdw 1.603 2.450 nonbonded pdb=" OE1 GLU A 866 " pdb=" HZ2 LYS A 868 " model vdw 1.605 2.450 ... (remaining 321298 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 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: 0.140 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.720 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3304 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 0.047 12334 Z= 0.229 Angle : 0.864 10.310 16970 Z= 0.501 Chirality : 0.054 0.913 1983 Planarity : 0.015 0.245 1955 Dihedral : 13.186 144.630 4817 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.67 % Allowed : 2.49 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.22 (0.22), residues: 1333 helix: 0.77 (0.18), residues: 672 sheet: -0.58 (0.37), residues: 180 loop : -0.28 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.066 0.006 ARG A 459 TYR 0.039 0.007 TYR A1676 PHE 0.055 0.004 PHE A 537 TRP 0.116 0.010 TRP A 316 HIS 0.016 0.003 HIS A1749 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.23 (12334) covalent geometry : angle 0.86424 / 0.50 (16970) hydrogen bonds : bond 0.13178 / 8.77 ( 621) hydrogen bonds : angle 5.40087 / 3.92 ( 1739) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 208 time to evaluate : 0.553 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ARG cc_start: 0.8394 (ttt180) cc_final: 0.7666 (mtm180) REVERT: A 272 MET cc_start: 0.7855 (mtp) cc_final: 0.7155 (mtp) REVERT: A 377 VAL cc_start: 0.8626 (t) cc_final: 0.8383 (m) REVERT: A 379 LYS cc_start: 0.8641 (mmtt) cc_final: 0.8277 (mmtm) REVERT: A 503 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7179 (mt-10) REVERT: A 710 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7581 (tp30) REVERT: A 897 MET cc_start: 0.5371 (mtm) cc_final: 0.4778 (tmm) REVERT: A 940 ASP cc_start: 0.2701 (OUTLIER) cc_final: 0.2307 (m-30) REVERT: A 1368 ARG cc_start: 0.4125 (mmt90) cc_final: 0.3898 (mpt-90) REVERT: A 1825 TRP cc_start: 0.2199 (t-100) cc_final: 0.1941 (t60) outliers start: 8 outliers final: 5 residues processed: 215 average time/residue: 0.2904 time to fit residues: 86.2398 Evaluate side-chains 174 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 168 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 940 ASP Chi-restraints excluded: chain D residue 364 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.0070 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.0370 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 HIS ** A1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 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 = 0.4622 r_free = 0.4622 target = 0.189816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.152675 restraints weight = 68009.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.160563 restraints weight = 30875.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.165664 restraints weight = 16882.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.168883 restraints weight = 10457.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.170915 restraints weight = 7214.954| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3595 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12334 Z= 0.132 Angle : 0.579 7.371 16970 Z= 0.306 Chirality : 0.043 0.761 1983 Planarity : 0.005 0.095 1955 Dihedral : 10.439 152.180 2150 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.67 % Allowed : 6.40 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.96 (0.23), residues: 1333 helix: 1.50 (0.19), residues: 673 sheet: -0.39 (0.38), residues: 182 loop : -0.05 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 353 TYR 0.016 0.001 TYR A1746 PHE 0.049 0.002 PHE A 142 TRP 0.012 0.002 TRP A 316 HIS 0.005 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (12334) covalent geometry : angle 0.57915 / 0.31 (16970) hydrogen bonds : bond 0.05274 / 3.63 ( 621) hydrogen bonds : angle 4.61790 / 3.31 ( 1739) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 178 time to evaluate : 0.616 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7927 (mtp) cc_final: 0.7260 (mtp) REVERT: A 379 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8137 (mttm) REVERT: A 503 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7225 (mt-10) REVERT: A 1800 LYS cc_start: 0.7531 (tttp) cc_final: 0.7216 (tptp) outliers start: 8 outliers final: 6 residues processed: 184 average time/residue: 0.2819 time to fit residues: 72.2369 Evaluate side-chains 172 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 166 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1722 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.190350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.153445 restraints weight = 67720.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.161429 restraints weight = 30767.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.166558 restraints weight = 16784.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.169718 restraints weight = 10340.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.171484 restraints weight = 7170.335| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3858 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12334 Z= 0.130 Angle : 0.559 8.234 16970 Z= 0.292 Chirality : 0.042 0.768 1983 Planarity : 0.004 0.044 1955 Dihedral : 10.188 155.584 2143 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.16 % Allowed : 6.82 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 1.02 (0.23), residues: 1333 helix: 1.48 (0.19), residues: 683 sheet: -0.61 (0.38), residues: 189 loop : 0.20 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 536 TYR 0.013 0.001 TYR A1695 PHE 0.038 0.002 PHE A 142 TRP 0.008 0.001 TRP A 316 HIS 0.004 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (12334) covalent geometry : angle 0.55942 / 0.29 (16970) hydrogen bonds : bond 0.04669 / 3.25 ( 621) hydrogen bonds : angle 4.39148 / 3.18 ( 1739) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 0.625 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASP cc_start: 0.6411 (m-30) cc_final: 0.5715 (p0) REVERT: A 272 MET cc_start: 0.7955 (mtp) cc_final: 0.7288 (mtp) REVERT: A 307 ARG cc_start: 0.7549 (ttt-90) cc_final: 0.7197 (ttp80) REVERT: A 379 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8131 (mmtt) REVERT: A 503 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7286 (mt-10) REVERT: A 1363 LYS cc_start: 0.7220 (mmtt) cc_final: 0.6926 (mptt) REVERT: A 1800 LYS cc_start: 0.7620 (tttp) cc_final: 0.7204 (tptp) REVERT: A 1816 ASP cc_start: 0.2524 (OUTLIER) cc_final: 0.2287 (t70) REVERT: A 1825 TRP cc_start: 0.2395 (t-100) cc_final: 0.0498 (t-100) outliers start: 14 outliers final: 12 residues processed: 190 average time/residue: 0.3005 time to fit residues: 78.8164 Evaluate side-chains 182 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1722 SER Chi-restraints excluded: chain A residue 1816 ASP Chi-restraints excluded: chain D residue 352 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 21 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 HIS ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN ** A1654 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 = 0.4623 r_free = 0.4623 target = 0.189160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.152706 restraints weight = 69075.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.160550 restraints weight = 31564.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.165617 restraints weight = 17277.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.168805 restraints weight = 10720.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.170855 restraints weight = 7410.061| |-----------------------------------------------------------------------------| r_work (final): 0.4405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4421 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12334 Z= 0.193 Angle : 0.676 11.632 16970 Z= 0.354 Chirality : 0.045 0.780 1983 Planarity : 0.005 0.050 1955 Dihedral : 10.405 159.340 2143 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 1.25 % Allowed : 8.15 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.47 (0.23), residues: 1333 helix: 1.06 (0.19), residues: 678 sheet: -1.09 (0.37), residues: 187 loop : 0.02 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 86 TYR 0.028 0.002 TYR A1828 PHE 0.038 0.002 PHE A 142 TRP 0.008 0.002 TRP A 138 HIS 0.008 0.001 HIS A1325 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (12334) covalent geometry : angle 0.67568 / 0.35 (16970) hydrogen bonds : bond 0.04790 / 3.31 ( 621) hydrogen bonds : angle 4.61364 / 3.31 ( 1739) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.355 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.8081 (mtp) cc_final: 0.7489 (mtp) REVERT: A 307 ARG cc_start: 0.7978 (ttt-90) cc_final: 0.7556 (ttp80) REVERT: A 371 LYS cc_start: 0.8780 (mmtm) cc_final: 0.8208 (tttt) REVERT: A 379 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8233 (mmtt) REVERT: A 503 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7446 (mt-10) REVERT: A 842 MET cc_start: 0.6984 (mmt) cc_final: 0.6751 (tpp) REVERT: A 1058 LEU cc_start: 0.4285 (OUTLIER) cc_final: 0.2278 (pp) REVERT: A 1316 GLU cc_start: 0.5670 (tt0) cc_final: 0.5162 (tm-30) REVERT: A 1363 LYS cc_start: 0.7438 (mmtt) cc_final: 0.7134 (mmtm) REVERT: A 1661 GLU cc_start: 0.7517 (tp30) cc_final: 0.7294 (tm-30) REVERT: A 1800 LYS cc_start: 0.7372 (tttp) cc_final: 0.6876 (tptp) REVERT: A 1804 ASP cc_start: 0.6810 (m-30) cc_final: 0.5990 (m-30) REVERT: A 1816 ASP cc_start: 0.3491 (OUTLIER) cc_final: 0.3195 (t70) REVERT: A 1854 MET cc_start: 0.6783 (mmm) cc_final: 0.6578 (mmm) outliers start: 15 outliers final: 12 residues processed: 196 average time/residue: 0.2668 time to fit residues: 73.0144 Evaluate side-chains 187 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1816 ASP Chi-restraints excluded: chain A residue 1822 GLU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 356 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 101 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 63 optimal weight: 0.0470 chunk 91 optimal weight: 0.9980 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 943 HIS ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 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 = 0.4606 r_free = 0.4606 target = 0.187327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.150751 restraints weight = 69110.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.158635 restraints weight = 31962.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.163867 restraints weight = 17765.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.167132 restraints weight = 10999.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.169232 restraints weight = 7576.835| |-----------------------------------------------------------------------------| r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4944 moved from start: 0.7296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 12334 Z= 0.239 Angle : 0.712 8.053 16970 Z= 0.387 Chirality : 0.047 0.780 1983 Planarity : 0.006 0.072 1955 Dihedral : 10.682 160.846 2141 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.97 % Rotamer: Outliers : 2.24 % Allowed : 10.81 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -0.25 (0.23), residues: 1333 helix: 0.55 (0.19), residues: 679 sheet: -1.38 (0.35), residues: 191 loop : -0.47 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 789 TYR 0.037 0.002 TYR A1828 PHE 0.040 0.003 PHE A 142 TRP 0.014 0.003 TRP A1380 HIS 0.013 0.002 HIS A1683 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.24 (12334) covalent geometry : angle 0.71215 / 0.39 (16970) hydrogen bonds : bond 0.05106 / 3.53 ( 621) hydrogen bonds : angle 5.04738 / 3.59 ( 1739) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.591 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7818 (tttp) REVERT: A 168 ASP cc_start: 0.7505 (m-30) cc_final: 0.6768 (p0) REVERT: A 268 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8018 (tm-30) REVERT: A 360 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7599 (mm-30) REVERT: A 371 LYS cc_start: 0.8813 (mmtm) cc_final: 0.8267 (tttp) REVERT: A 503 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7594 (mt-10) REVERT: A 1036 GLU cc_start: 0.6920 (tp30) cc_final: 0.6337 (tp30) REVERT: A 1582 LEU cc_start: 0.8082 (mt) cc_final: 0.7762 (mt) REVERT: A 1802 MET cc_start: 0.6536 (mmp) cc_final: 0.6281 (mmp) REVERT: A 1816 ASP cc_start: 0.3576 (OUTLIER) cc_final: 0.3179 (t70) outliers start: 27 outliers final: 20 residues processed: 216 average time/residue: 0.2574 time to fit residues: 78.1402 Evaluate side-chains 206 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 771 TYR Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 791 LYS Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1748 TYR Chi-restraints excluded: chain A residue 1816 ASP Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 355 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 84 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 58 optimal weight: 0.0170 chunk 52 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 62 optimal weight: 0.0270 chunk 96 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1770 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.188188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.150744 restraints weight = 70678.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.158771 restraints weight = 33175.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.164062 restraints weight = 18447.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.167172 restraints weight = 11527.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.169372 restraints weight = 8072.369| |-----------------------------------------------------------------------------| r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5073 moved from start: 0.8238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12334 Z= 0.168 Angle : 0.595 7.555 16970 Z= 0.317 Chirality : 0.043 0.780 1983 Planarity : 0.006 0.073 1955 Dihedral : 10.631 161.502 2141 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.66 % Allowed : 12.14 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.02 (0.23), residues: 1333 helix: 0.89 (0.20), residues: 680 sheet: -1.30 (0.35), residues: 204 loop : -0.52 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 307 TYR 0.020 0.002 TYR A1828 PHE 0.023 0.002 PHE A 142 TRP 0.007 0.002 TRP A 138 HIS 0.006 0.001 HIS A1683 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (12334) covalent geometry : angle 0.59461 / 0.32 (16970) hydrogen bonds : bond 0.04548 / 3.18 ( 621) hydrogen bonds : angle 4.73264 / 3.42 ( 1739) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.551 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7982 (tttp) REVERT: A 83 HIS cc_start: 0.8652 (OUTLIER) cc_final: 0.8169 (p90) REVERT: A 140 GLN cc_start: 0.6911 (OUTLIER) cc_final: 0.6549 (pm20) REVERT: A 268 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8005 (tm-30) REVERT: A 371 LYS cc_start: 0.8898 (mmtm) cc_final: 0.8422 (tttp) REVERT: A 379 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8318 (mmtt) REVERT: A 503 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7655 (mt-10) REVERT: A 684 MET cc_start: 0.6137 (mpp) cc_final: 0.5822 (mpp) REVERT: A 747 GLN cc_start: 0.7387 (tp40) cc_final: 0.6849 (tm-30) REVERT: A 771 TYR cc_start: 0.4107 (OUTLIER) cc_final: 0.1607 (m-10) REVERT: A 1036 GLU cc_start: 0.6715 (tp30) cc_final: 0.6141 (tp30) REVERT: A 1356 LEU cc_start: 0.8656 (mt) cc_final: 0.8392 (mt) REVERT: A 1545 HIS cc_start: 0.3629 (OUTLIER) cc_final: 0.2681 (m-70) REVERT: A 1802 MET cc_start: 0.6633 (mmp) cc_final: 0.6375 (mmp) REVERT: A 1816 ASP cc_start: 0.3353 (OUTLIER) cc_final: 0.1658 (p0) REVERT: A 1833 GLN cc_start: 0.7302 (tt0) cc_final: 0.6838 (tt0) outliers start: 32 outliers final: 25 residues processed: 211 average time/residue: 0.2455 time to fit residues: 73.2148 Evaluate side-chains 214 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 771 TYR Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 790 ARG Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1545 HIS Chi-restraints excluded: chain A residue 1580 CYS Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1693 ASP Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain A residue 1816 ASP Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 355 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 98 optimal weight: 0.0870 chunk 103 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 40 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.188352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.151252 restraints weight = 70428.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.159358 restraints weight = 32868.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.164538 restraints weight = 18178.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.167773 restraints weight = 11361.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.169859 restraints weight = 7917.990| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5138 moved from start: 0.8884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 12334 Z= 0.136 Angle : 0.578 9.944 16970 Z= 0.302 Chirality : 0.042 0.777 1983 Planarity : 0.005 0.064 1955 Dihedral : 10.489 161.970 2141 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.49 % Allowed : 13.05 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.26 (0.24), residues: 1333 helix: 1.13 (0.20), residues: 682 sheet: -1.14 (0.36), residues: 194 loop : -0.53 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 307 TYR 0.019 0.001 TYR A 267 PHE 0.037 0.002 PHE A 894 TRP 0.013 0.002 TRP A 316 HIS 0.006 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (12334) covalent geometry : angle 0.57820 / 0.30 (16970) hydrogen bonds : bond 0.04176 / 2.89 ( 621) hydrogen bonds : angle 4.53333 / 3.30 ( 1739) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.595 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8384 (mtpt) cc_final: 0.7902 (ttpp) REVERT: A 109 GLN cc_start: 0.7502 (tp-100) cc_final: 0.6949 (tp40) REVERT: A 140 GLN cc_start: 0.6946 (OUTLIER) cc_final: 0.6605 (pm20) REVERT: A 272 MET cc_start: 0.8357 (mtp) cc_final: 0.7796 (mtp) REVERT: A 307 ARG cc_start: 0.8416 (ttp80) cc_final: 0.8163 (ttp80) REVERT: A 316 TRP cc_start: 0.6587 (t60) cc_final: 0.5929 (t60) REVERT: A 360 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7694 (mm-30) REVERT: A 371 LYS cc_start: 0.8889 (mmtm) cc_final: 0.8439 (tttt) REVERT: A 379 LYS cc_start: 0.8804 (mmtt) cc_final: 0.8313 (mmtt) REVERT: A 503 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7638 (mt-10) REVERT: A 640 ARG cc_start: 0.3932 (ttp80) cc_final: 0.3687 (ttp80) REVERT: A 747 GLN cc_start: 0.7464 (tp40) cc_final: 0.6980 (tm-30) REVERT: A 771 TYR cc_start: 0.4261 (OUTLIER) cc_final: 0.2012 (m-10) REVERT: A 1317 MET cc_start: 0.5424 (mtp) cc_final: 0.5163 (mtp) REVERT: A 1356 LEU cc_start: 0.8675 (mt) cc_final: 0.8378 (mt) REVERT: A 1802 MET cc_start: 0.6824 (mmp) cc_final: 0.6589 (mmp) REVERT: A 1816 ASP cc_start: 0.3549 (OUTLIER) cc_final: 0.1984 (t70) outliers start: 30 outliers final: 22 residues processed: 215 average time/residue: 0.2533 time to fit residues: 77.0649 Evaluate side-chains 215 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 HIS Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 771 TYR Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 791 LYS Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 975 LYS Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1346 MET Chi-restraints excluded: chain A residue 1545 HIS Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1687 HIS Chi-restraints excluded: chain A residue 1816 ASP Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 355 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 44 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 0.0060 chunk 132 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 119 optimal weight: 0.1980 chunk 92 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.188256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.150702 restraints weight = 70614.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.158819 restraints weight = 33117.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.164116 restraints weight = 18399.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.167454 restraints weight = 11558.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.169287 restraints weight = 8070.854| |-----------------------------------------------------------------------------| r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5212 moved from start: 0.9302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 12334 Z= 0.124 Angle : 0.547 8.924 16970 Z= 0.287 Chirality : 0.041 0.778 1983 Planarity : 0.005 0.056 1955 Dihedral : 10.437 162.164 2141 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.41 % Allowed : 13.97 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.41 (0.24), residues: 1333 helix: 1.28 (0.20), residues: 684 sheet: -1.21 (0.36), residues: 199 loop : -0.45 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 307 TYR 0.013 0.001 TYR A1828 PHE 0.020 0.002 PHE A 142 TRP 0.012 0.002 TRP A 316 HIS 0.005 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (12334) covalent geometry : angle 0.54721 / 0.29 (16970) hydrogen bonds : bond 0.04065 / 2.84 ( 621) hydrogen bonds : angle 4.40725 / 3.21 ( 1739) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.575 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLN cc_start: 0.7483 (tp-100) cc_final: 0.7251 (tp40) REVERT: A 140 GLN cc_start: 0.6998 (OUTLIER) cc_final: 0.6643 (pm20) REVERT: A 269 ARG cc_start: 0.8704 (ttt180) cc_final: 0.8398 (mtt180) REVERT: A 272 MET cc_start: 0.8374 (mtp) cc_final: 0.7815 (mtp) REVERT: A 316 TRP cc_start: 0.6637 (t60) cc_final: 0.5971 (t60) REVERT: A 360 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7683 (mm-30) REVERT: A 371 LYS cc_start: 0.8922 (mmtm) cc_final: 0.8467 (tttp) REVERT: A 379 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8310 (mmtt) REVERT: A 503 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7695 (mt-10) REVERT: A 548 GLN cc_start: 0.6499 (mp10) cc_final: 0.6094 (mt0) REVERT: A 747 GLN cc_start: 0.7585 (tp40) cc_final: 0.7014 (tm-30) REVERT: A 771 TYR cc_start: 0.4398 (OUTLIER) cc_final: 0.2131 (m-10) REVERT: A 897 MET cc_start: 0.5606 (mtt) cc_final: 0.5235 (ttm) REVERT: A 1317 MET cc_start: 0.5728 (mtp) cc_final: 0.5256 (mtp) REVERT: A 1356 LEU cc_start: 0.8693 (mt) cc_final: 0.8423 (mt) REVERT: A 1545 HIS cc_start: 0.3382 (OUTLIER) cc_final: 0.2388 (m-70) REVERT: A 1816 ASP cc_start: 0.3778 (OUTLIER) cc_final: 0.2370 (p0) outliers start: 29 outliers final: 23 residues processed: 214 average time/residue: 0.2646 time to fit residues: 80.5119 Evaluate side-chains 221 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 92 HIS Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 771 TYR Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 790 ARG Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 975 LYS Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1545 HIS Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1687 HIS Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain A residue 1816 ASP Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 355 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 17 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 111 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.185045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.147422 restraints weight = 71365.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.155598 restraints weight = 33471.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.160608 restraints weight = 18679.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.164050 restraints weight = 11892.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.165986 restraints weight = 8318.859| |-----------------------------------------------------------------------------| r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5430 moved from start: 1.0272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 12334 Z= 0.161 Angle : 0.594 8.891 16970 Z= 0.317 Chirality : 0.042 0.781 1983 Planarity : 0.005 0.063 1955 Dihedral : 10.571 162.256 2141 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.66 % Allowed : 14.30 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.20 (0.23), residues: 1333 helix: 1.05 (0.20), residues: 683 sheet: -1.08 (0.36), residues: 192 loop : -0.57 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 307 TYR 0.026 0.002 TYR A1746 PHE 0.018 0.002 PHE A 142 TRP 0.012 0.002 TRP A 316 HIS 0.005 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (12334) covalent geometry : angle 0.59432 / 0.32 (16970) hydrogen bonds : bond 0.04292 / 3.02 ( 621) hydrogen bonds : angle 4.53455 / 3.32 ( 1739) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Evaluate side-chains 243 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 0.687 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8563 (mtpt) cc_final: 0.8054 (ttpp) REVERT: A 109 GLN cc_start: 0.7570 (tp-100) cc_final: 0.7315 (tp40) REVERT: A 140 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6690 (pm20) REVERT: A 217 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6570 (pm20) REVERT: A 224 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8534 (mp10) REVERT: A 225 LYS cc_start: 0.8472 (ttpp) cc_final: 0.8267 (tmtt) REVERT: A 272 MET cc_start: 0.8418 (mtp) cc_final: 0.7916 (mtp) REVERT: A 360 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7725 (mm-30) REVERT: A 369 ASP cc_start: 0.7438 (t0) cc_final: 0.6967 (t70) REVERT: A 371 LYS cc_start: 0.8978 (mmtm) cc_final: 0.8483 (tttp) REVERT: A 379 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8340 (mmtt) REVERT: A 503 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7680 (mt-10) REVERT: A 747 GLN cc_start: 0.7676 (tp40) cc_final: 0.7186 (tm-30) REVERT: A 771 TYR cc_start: 0.4528 (OUTLIER) cc_final: 0.2479 (m-10) REVERT: A 834 SER cc_start: 0.7174 (p) cc_final: 0.6922 (t) REVERT: A 895 LYS cc_start: 0.8226 (mmmm) cc_final: 0.7996 (mmmm) REVERT: A 897 MET cc_start: 0.5841 (mtt) cc_final: 0.5470 (ttm) REVERT: A 996 ARG cc_start: 0.6527 (mtm-85) cc_final: 0.6159 (mtm-85) REVERT: A 1380 TRP cc_start: 0.5295 (t60) cc_final: 0.4489 (t60) REVERT: A 1760 PHE cc_start: 0.8327 (t80) cc_final: 0.7962 (t80) REVERT: A 1802 MET cc_start: 0.7076 (mmp) cc_final: 0.6384 (mmp) REVERT: A 1807 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6894 (mt-10) REVERT: A 1816 ASP cc_start: 0.4112 (OUTLIER) cc_final: 0.2946 (p0) outliers start: 32 outliers final: 26 residues processed: 232 average time/residue: 0.2712 time to fit residues: 88.2150 Evaluate side-chains 227 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 92 HIS Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 771 TYR Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 790 ARG Chi-restraints excluded: chain A residue 791 LYS Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 975 LYS Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1545 HIS Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1687 HIS Chi-restraints excluded: chain A residue 1816 ASP Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 355 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 84 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.182314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.144927 restraints weight = 70913.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.152948 restraints weight = 33349.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.158061 restraints weight = 18627.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.161306 restraints weight = 11761.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.163283 restraints weight = 8292.922| |-----------------------------------------------------------------------------| r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5703 moved from start: 1.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 12334 Z= 0.227 Angle : 0.679 9.422 16970 Z= 0.373 Chirality : 0.046 0.785 1983 Planarity : 0.007 0.096 1955 Dihedral : 10.987 162.898 2141 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.48 % Favored : 94.45 % Rotamer: Outliers : 2.58 % Allowed : 15.71 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -0.64 (0.23), residues: 1333 helix: 0.41 (0.19), residues: 685 sheet: -1.57 (0.35), residues: 202 loop : -0.97 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 86 TYR 0.029 0.002 TYR A1828 PHE 0.027 0.003 PHE A 894 TRP 0.019 0.003 TRP A1825 HIS 0.007 0.001 HIS A1713 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.23 (12334) covalent geometry : angle 0.67915 / 0.37 (16970) hydrogen bonds : bond 0.05052 / 3.61 ( 621) hydrogen bonds : angle 5.00071 / 3.66 ( 1739) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 0.554 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8742 (mtpt) cc_final: 0.8259 (ttpp) REVERT: A 78 THR cc_start: 0.8145 (m) cc_final: 0.7896 (p) REVERT: A 138 TRP cc_start: 0.7267 (m100) cc_final: 0.6681 (m100) REVERT: A 140 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6942 (pm20) REVERT: A 168 ASP cc_start: 0.7839 (m-30) cc_final: 0.7331 (t0) REVERT: A 217 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6930 (pm20) REVERT: A 224 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8552 (mp10) REVERT: A 268 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8201 (tm-30) REVERT: A 269 ARG cc_start: 0.8876 (ttt180) cc_final: 0.8101 (mtt180) REVERT: A 273 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7753 (mm-30) REVERT: A 316 TRP cc_start: 0.6954 (t60) cc_final: 0.6139 (t60) REVERT: A 321 VAL cc_start: 0.8588 (t) cc_final: 0.8283 (p) REVERT: A 360 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7975 (mm-30) REVERT: A 369 ASP cc_start: 0.7736 (t0) cc_final: 0.7335 (t70) REVERT: A 371 LYS cc_start: 0.9028 (mmtm) cc_final: 0.8602 (tttt) REVERT: A 379 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8298 (mttm) REVERT: A 462 LYS cc_start: 0.8757 (ptmm) cc_final: 0.8499 (ptmm) REVERT: A 503 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7724 (mt-10) REVERT: A 637 TYR cc_start: 0.7276 (t80) cc_final: 0.7026 (t80) REVERT: A 771 TYR cc_start: 0.5006 (OUTLIER) cc_final: 0.2694 (m-10) REVERT: A 895 LYS cc_start: 0.8413 (mmmm) cc_final: 0.7527 (mmmt) REVERT: A 896 PHE cc_start: 0.7862 (t80) cc_final: 0.7482 (t80) REVERT: A 899 ASP cc_start: 0.8044 (m-30) cc_final: 0.7725 (m-30) REVERT: A 925 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6817 (tm-30) REVERT: A 945 PHE cc_start: 0.7197 (m-80) cc_final: 0.6921 (m-80) REVERT: A 996 ARG cc_start: 0.7095 (mtm-85) cc_final: 0.6651 (mtm-85) REVERT: A 1073 GLN cc_start: 0.7614 (tp40) cc_final: 0.7385 (tp40) REVERT: A 1355 ASN cc_start: 0.8483 (t0) cc_final: 0.7991 (t0) REVERT: A 1358 ARG cc_start: 0.7859 (mmt180) cc_final: 0.7434 (mmt-90) REVERT: A 1359 LEU cc_start: 0.7831 (mt) cc_final: 0.7376 (mt) REVERT: A 1380 TRP cc_start: 0.5672 (t60) cc_final: 0.5377 (t60) REVERT: A 1672 LYS cc_start: 0.7716 (pptt) cc_final: 0.6532 (mttt) REVERT: A 1802 MET cc_start: 0.7327 (mmp) cc_final: 0.6621 (mmp) REVERT: A 1816 ASP cc_start: 0.4713 (OUTLIER) cc_final: 0.3942 (t70) REVERT: A 1854 MET cc_start: 0.7129 (mmm) cc_final: 0.6718 (mmm) outliers start: 31 outliers final: 25 residues processed: 247 average time/residue: 0.2548 time to fit residues: 88.9300 Evaluate side-chains 250 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 HIS Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 356 HIS Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 771 TYR Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 790 ARG Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1545 HIS Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1687 HIS Chi-restraints excluded: chain A residue 1693 ASP Chi-restraints excluded: chain A residue 1761 HIS Chi-restraints excluded: chain A residue 1816 ASP Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 355 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1355 ASN ** D 356 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 = 0.4556 r_free = 0.4556 target = 0.184490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.146336 restraints weight = 70859.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.154245 restraints weight = 33595.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.159339 restraints weight = 18956.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.162585 restraints weight = 12096.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.164544 restraints weight = 8633.196| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5806 moved from start: 1.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 12334 Z= 0.204 Angle : 0.648 9.352 16970 Z= 0.349 Chirality : 0.044 0.783 1983 Planarity : 0.006 0.066 1955 Dihedral : 11.005 163.323 2141 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.70 % Favored : 94.22 % Rotamer: Outliers : 2.49 % Allowed : 17.21 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -0.67 (0.23), residues: 1333 helix: 0.42 (0.19), residues: 684 sheet: -1.68 (0.35), residues: 202 loop : -1.00 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 459 TYR 0.024 0.002 TYR A 769 PHE 0.025 0.002 PHE A1671 TRP 0.015 0.003 TRP A 316 HIS 0.008 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 (12334) covalent geometry : angle 0.64827 / 0.35 (16970) hydrogen bonds : bond 0.04761 / 3.43 ( 621) hydrogen bonds : angle 4.93307 / 3.61 ( 1739) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4114.64 seconds wall clock time: 71 minutes 3.41 seconds (4263.41 seconds total)