Starting phenix.real_space_refine on Sun Jul 5 07:45:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zpk_14856/07_2026/7zpk_14856.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zpk_14856/07_2026/7zpk_14856.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 { model { file = "/net/cci-nas-00/data/ceres_data/7zpk_14856/07_2026/7zpk_14856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zpk_14856/07_2026/7zpk_14856.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zpk_14856/07_2026/7zpk_14856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zpk_14856/07_2026/7zpk_14856.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zpk_14856/07_2026/7zpk_14856.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zpk_14856/07_2026/7zpk_14856.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= 0.018 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 70 5.16 5 C 8185 2.51 5 N 2263 2.21 5 O 2602 1.98 5 H 12760 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: 25935 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 20620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1280, 20620 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: "C" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3552 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 221} Chain breaks: 2 Time building chain proxies: 3.59, per 1000 atoms: 0.14 Number of scatterers: 25935 At special positions: 0 Unit cell: (97.695, 123.58, 162.825, 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 70 16.00 P 55 15.00 O 2602 8.00 N 2263 7.00 C 8185 6.00 H 12760 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: 2.34 Conformation dependent library (CDL) restraints added in 724.7 milliseconds 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2888 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 12 sheets defined 53.5% alpha, 13.9% beta 18 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 66 through 82 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 89 through 93 removed outlier: 3.823A pdb=" N ALA A 93 " --> pdb=" O ASN A 90 " (cutoff:3.500A) 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: 3.865A 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 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 184 through 196 removed outlier: 4.283A pdb=" N GLU A 188 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 231 removed outlier: 5.021A 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: 3.803A 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: 3.609A 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: 3.564A 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 519 through 524 Processing helix chain 'A' and resid 542 through 551 Processing helix chain 'A' and resid 565 through 592 removed outlier: 4.046A pdb=" N LYS A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER A 571 " --> pdb=" O ASP A 567 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU A 574 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 641 removed outlier: 4.242A pdb=" N GLY A 632 " --> pdb=" O ASN A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 706 removed outlier: 3.591A 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: 4.041A 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 1352 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: 7.893A pdb=" N GLU A1572 " --> pdb=" O THR A1568 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ARG A1573 " --> pdb=" O SER A1569 " (cutoff:3.500A) removed outlier: 4.147A 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: 3.616A pdb=" N LYS A1666 " --> pdb=" O THR A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1674 through 1682 removed outlier: 3.758A pdb=" N LEU A1678 " --> pdb=" O LYS A1674 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1716 removed outlier: 3.622A pdb=" N PHE A1700 " --> pdb=" O GLN A1696 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A1701 " --> pdb=" O ARG A1697 " (cutoff:3.500A) removed outlier: 3.634A 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: 4.011A pdb=" N TYR A1751 " --> pdb=" O ASP A1747 " (cutoff:3.500A) Processing helix chain 'A' and resid 1756 through 1772 removed outlier: 3.724A pdb=" N LYS A1768 " --> pdb=" O ASP A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1799 through 1817 removed outlier: 3.970A pdb=" N GLY A1803 " --> pdb=" O PRO A1799 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1842 Proline residue: A1830 - end of helix Proline residue: A1834 - end of helix removed outlier: 3.695A 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 'C' and resid 18 through 26 Processing helix chain 'C' and resid 30 through 42 Processing helix chain 'C' and resid 79 through 95 Processing helix chain 'C' and resid 158 through 170 Processing helix chain 'C' and resid 185 through 189 removed outlier: 4.159A pdb=" N LYS C 189 " --> pdb=" O ALA C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 225 Processing helix chain 'C' and resid 292 through 304 Processing helix chain 'C' and resid 342 through 364 Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.931A pdb=" N THR A 151 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR A 96 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N MET A 150 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N PHE A 98 " --> pdb=" O MET A 150 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ARG A 95 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A 171 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A 175 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR A 60 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR A 206 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL A 62 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 6.134A 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: 6.094A pdb=" N CYS A 251 " --> pdb=" O TYR A 560 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N MET A 562 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE A 253 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ALA A 564 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL A 255 " --> pdb=" O ALA A 564 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE A 445 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.680A 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 removed outlier: 3.731A pdb=" N GLN A 747 " --> pdb=" O ILE A1550 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 816 through 820 removed outlier: 3.692A pdb=" N PHE A 816 " --> pdb=" O ILE A 827 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLU A 824 " --> pdb=" O THR A 778 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 778 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 832 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU A 770 " --> pdb=" O LYS A 832 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER A 834 " --> pdb=" O CYS A 768 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS A 768 " --> pdb=" O SER A 834 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N PHE A 802 " --> pdb=" O ILE A 773 " (cutoff:3.500A) removed outlier: 4.671A 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: 3.502A pdb=" N LEU A 987 " --> pdb=" O TYR A 951 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP A 949 " --> pdb=" O ASP A 989 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP A 991 " --> pdb=" O VAL A 947 " (cutoff:3.500A) removed outlier: 5.715A 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 'C' and resid 47 through 56 removed outlier: 5.716A pdb=" N TYR C 48 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N THR C 67 " --> pdb=" O TYR C 48 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU C 50 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG C 65 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN C 56 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 176 through 183 removed outlier: 5.657A pdb=" N TYR C 177 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ARG C 196 " --> pdb=" O TYR C 177 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL C 179 " --> pdb=" O THR C 194 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR C 194 " --> pdb=" O VAL C 179 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 308 through 312 662 hydrogen bonds defined for protein. 1896 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 6.20 Time building geometry restraints manager: 3.16 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: 12716 1.02 - 1.21: 44 1.21 - 1.41: 5449 1.41 - 1.61: 8015 1.61 - 1.81: 96 Bond restraints: 26320 Sorted by residual: bond pdb=" NH1 ARG A 86 " pdb="HH12 ARG A 86 " ideal model delta sigma weight residual 0.860 0.816 0.044 2.00e-02 2.50e+03 4.88e+00 bond pdb=" NE2 GLN A 985 " pdb="HE22 GLN A 985 " ideal model delta sigma weight residual 0.860 0.826 0.034 2.00e-02 2.50e+03 2.90e+00 bond pdb=" NH1 ARG A 640 " pdb="HH12 ARG A 640 " ideal model delta sigma weight residual 0.860 0.830 0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" NH2 ARG A 95 " pdb="HH22 ARG A 95 " ideal model delta sigma weight residual 0.860 0.832 0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" NH2 ARG A 201 " pdb="HH22 ARG A 201 " ideal model delta sigma weight residual 0.860 0.832 0.028 2.00e-02 2.50e+03 1.94e+00 ... (remaining 26315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.21: 47676 7.21 - 14.42: 7 14.42 - 21.63: 0 21.63 - 28.84: 1 28.84 - 36.05: 5 Bond angle restraints: 47689 Sorted by residual: angle pdb=" N ALA A 464 " pdb=" CA ALA A 464 " pdb=" HA ALA A 464 " ideal model delta sigma weight residual 110.00 73.95 36.05 3.00e+00 1.11e-01 1.44e+02 angle pdb=" CB ALA A 464 " pdb=" CA ALA A 464 " pdb=" HA ALA A 464 " ideal model delta sigma weight residual 109.00 73.14 35.86 3.00e+00 1.11e-01 1.43e+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 75.66 33.34 3.00e+00 1.11e-01 1.24e+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 77.45 31.55 3.00e+00 1.11e-01 1.11e+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 79.49 29.51 3.00e+00 1.11e-01 9.68e+01 ... (remaining 47684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 11920 35.86 - 71.71: 301 71.71 - 107.56: 15 107.56 - 143.42: 1 143.42 - 179.27: 9 Dihedral angle restraints: 12246 sinusoidal: 7092 harmonic: 5154 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 47.46 152.54 1 1.50e+01 4.44e-03 8.05e+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 64.28 135.72 1 1.50e+01 4.44e-03 7.32e+01 dihedral pdb=" O4' G B 26 " pdb=" C4' G B 26 " pdb=" C3' G B 26 " pdb=" C2' G B 26 " ideal model delta sinusoidal sigma weight residual -35.00 -8.97 -26.03 1 8.00e+00 1.56e-02 1.52e+01 ... (remaining 12243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 2158 0.164 - 0.327: 10 0.327 - 0.491: 0 0.491 - 0.655: 0 0.655 - 0.818: 1 Chirality restraints: 2169 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 -1.66 -0.82 2.00e-01 2.50e+01 1.67e+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 2.17 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" C1' A B 13 " pdb=" O4' A B 13 " pdb=" C2' A B 13 " pdb=" N9 A B 13 " both_signs ideal model delta sigma weight residual False 2.46 2.17 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 2166 not shown) Planarity restraints: 3621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 86 " -0.322 9.50e-02 1.11e+02 1.32e-01 1.43e+02 pdb=" NE ARG A 86 " -0.079 2.00e-02 2.50e+03 pdb=" CZ ARG A 86 " 0.077 2.00e-02 2.50e+03 pdb=" NH1 ARG A 86 " 0.136 2.00e-02 2.50e+03 pdb=" NH2 ARG A 86 " 0.043 2.00e-02 2.50e+03 pdb="HH11 ARG A 86 " 0.015 2.00e-02 2.50e+03 pdb="HH12 ARG A 86 " -0.134 2.00e-02 2.50e+03 pdb="HH21 ARG A 86 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 86 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 640 " -0.385 9.50e-02 1.11e+02 1.45e-01 1.16e+02 pdb=" NE ARG A 640 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 640 " 0.064 2.00e-02 2.50e+03 pdb=" NH1 ARG A 640 " 0.117 2.00e-02 2.50e+03 pdb=" NH2 ARG A 640 " 0.055 2.00e-02 2.50e+03 pdb="HH11 ARG A 640 " 0.008 2.00e-02 2.50e+03 pdb="HH12 ARG A 640 " -0.107 2.00e-02 2.50e+03 pdb="HH21 ARG A 640 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 640 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 95 " -0.515 9.50e-02 1.11e+02 1.80e-01 9.84e+01 pdb=" NE ARG A 95 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 95 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG A 95 " 0.044 2.00e-02 2.50e+03 pdb=" NH2 ARG A 95 " 0.105 2.00e-02 2.50e+03 pdb="HH11 ARG A 95 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 95 " -0.024 2.00e-02 2.50e+03 pdb="HH21 ARG A 95 " 0.007 2.00e-02 2.50e+03 pdb="HH22 ARG A 95 " -0.108 2.00e-02 2.50e+03 ... (remaining 3618 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1345 2.20 - 2.80: 53350 2.80 - 3.40: 71433 3.40 - 4.00: 90191 4.00 - 4.60: 139687 Nonbonded interactions: 356006 Sorted by model distance: nonbonded pdb=" OD2 ASP A1543 " pdb=" HG1 THR A1546 " model vdw 1.602 2.450 nonbonded pdb=" H LYS A 868 " pdb=" O GLY A1384 " model vdw 1.603 2.450 nonbonded pdb=" HG1 THR A1867 " pdb=" OD1 ASP A1869 " model vdw 1.612 2.450 nonbonded pdb=" HG SER A 915 " pdb=" OE1 GLU A 917 " model vdw 1.613 2.450 nonbonded pdb=" O LEU A1678 " pdb=" HG1 THR A1682 " model vdw 1.622 2.450 ... (remaining 356001 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: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.020 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5458 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 0.039 13560 Z= 0.168 Angle : 0.806 10.438 18621 Z= 0.458 Chirality : 0.051 0.818 2169 Planarity : 0.015 0.212 2167 Dihedral : 13.250 152.539 5286 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.68 % Allowed : 3.08 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.04 (0.21), residues: 1487 helix: 0.55 (0.17), residues: 738 sheet: -0.44 (0.35), residues: 201 loop : -0.32 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.051 0.006 ARG A 459 TYR 0.046 0.007 TYR A1695 PHE 0.033 0.004 PHE C 306 TRP 0.043 0.007 TRP A 316 HIS 0.015 0.003 HIS A1749 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (13560) covalent geometry : angle 0.80641 / 0.46 (18621) hydrogen bonds : bond 0.12842 / 8.38 ( 704) hydrogen bonds : angle 5.69925 / 4.08 ( 1968) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 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 232 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 223 time to evaluate : 0.463 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 230 LEU cc_start: 0.8242 (mm) cc_final: 0.7934 (mm) REVERT: A 381 LEU cc_start: 0.9665 (mt) cc_final: 0.9367 (tp) REVERT: A 637 TYR cc_start: 0.8382 (t80) cc_final: 0.8179 (t80) REVERT: A 813 ILE cc_start: 0.6817 (pt) cc_final: 0.6603 (mt) REVERT: A 1674 LYS cc_start: 0.7797 (mmtt) cc_final: 0.6298 (mmtt) REVERT: A 1764 ASP cc_start: 0.7695 (m-30) cc_final: 0.7436 (m-30) outliers start: 9 outliers final: 3 residues processed: 231 average time/residue: 0.2577 time to fit residues: 83.2052 Evaluate side-chains 162 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 159 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 364 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 HIS ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN ** A1545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** 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 = 0.4039 r_free = 0.4039 target = 0.077483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.054121 restraints weight = 403821.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.055655 restraints weight = 265534.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.056795 restraints weight = 199752.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.057110 restraints weight = 165015.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.057881 restraints weight = 151488.034| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 13560 Z= 0.315 Angle : 0.881 9.583 18621 Z= 0.470 Chirality : 0.049 0.837 2169 Planarity : 0.008 0.118 2167 Dihedral : 10.710 155.862 2310 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 23.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.83 % Favored : 96.10 % Rotamer: Outliers : 2.33 % Allowed : 6.91 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.50 (0.21), residues: 1487 helix: 0.10 (0.18), residues: 752 sheet: -1.05 (0.32), residues: 219 loop : -0.37 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 640 TYR 0.035 0.003 TYR A1566 PHE 0.026 0.003 PHE A 98 TRP 0.021 0.003 TRP A1825 HIS 0.011 0.003 HIS A1325 Details of bonding type rmsd/Z covalent geometry : bond 0.00652 / 0.31 (13560) covalent geometry : angle 0.88125 / 0.47 (18621) hydrogen bonds : bond 0.07863 / 5.10 ( 704) hydrogen bonds : angle 5.58543 / 4.05 ( 1968) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 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 181 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.690 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: 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 306 CYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8983 (p) REVERT: A 471 LEU cc_start: 0.8286 (mt) cc_final: 0.8020 (mt) REVERT: A 562 MET cc_start: 0.6071 (tpp) cc_final: 0.5808 (tpp) REVERT: A 1557 ASP cc_start: 0.7720 (m-30) cc_final: 0.7357 (m-30) REVERT: A 1560 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6594 (mt-10) REVERT: A 1683 HIS cc_start: 0.8232 (t-90) cc_final: 0.7552 (t70) REVERT: A 1695 TYR cc_start: 0.8383 (p90) cc_final: 0.8048 (p90) REVERT: A 1755 VAL cc_start: 0.8750 (t) cc_final: 0.7938 (t) REVERT: A 1760 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8479 (m-80) REVERT: A 1764 ASP cc_start: 0.8320 (m-30) cc_final: 0.8005 (m-30) outliers start: 31 outliers final: 23 residues processed: 166 average time/residue: 0.2554 time to fit residues: 60.3041 Evaluate side-chains 149 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 771 TYR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 850 HIS Chi-restraints excluded: chain A residue 874 SER Chi-restraints excluded: chain A residue 886 ASP Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 1566 TYR Chi-restraints excluded: chain A residue 1572 GLU Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1713 HIS Chi-restraints excluded: chain A residue 1731 SER Chi-restraints excluded: chain A residue 1760 PHE Chi-restraints excluded: chain A residue 1772 GLU Chi-restraints excluded: chain A residue 1821 LEU Chi-restraints excluded: chain C residue 342 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 71 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 chunk 118 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.075260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.049546 restraints weight = 280599.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.051131 restraints weight = 181659.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.052282 restraints weight = 134479.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.052996 restraints weight = 109596.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.053674 restraints weight = 96301.240| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13560 Z= 0.135 Angle : 0.580 7.459 18621 Z= 0.304 Chirality : 0.042 0.788 2169 Planarity : 0.005 0.055 2167 Dihedral : 10.228 159.414 2309 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.50 % Allowed : 9.53 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.39 (0.21), residues: 1487 helix: 0.96 (0.18), residues: 758 sheet: -0.63 (0.34), residues: 206 loop : -0.23 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1060 TYR 0.015 0.001 TYR A1891 PHE 0.014 0.002 PHE A 72 TRP 0.010 0.001 TRP A 316 HIS 0.008 0.001 HIS A1325 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (13560) covalent geometry : angle 0.57993 / 0.30 (18621) hydrogen bonds : bond 0.05170 / 3.32 ( 704) hydrogen bonds : angle 4.84473 / 3.53 ( 1968) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 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 152 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.667 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 TYR cc_start: 0.9489 (m-10) cc_final: 0.9266 (m-10) REVERT: A 1344 SER cc_start: 0.9141 (t) cc_final: 0.8907 (m) REVERT: A 1557 ASP cc_start: 0.7752 (m-30) cc_final: 0.7435 (m-30) REVERT: A 1560 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6714 (mt-10) REVERT: A 1683 HIS cc_start: 0.8220 (t-90) cc_final: 0.7461 (t70) REVERT: A 1695 TYR cc_start: 0.8263 (p90) cc_final: 0.7784 (p90) REVERT: A 1755 VAL cc_start: 0.8720 (t) cc_final: 0.8499 (t) REVERT: A 1831 MET cc_start: 0.6862 (mmt) cc_final: 0.6507 (mmt) outliers start: 20 outliers final: 17 residues processed: 144 average time/residue: 0.3036 time to fit residues: 61.7348 Evaluate side-chains 139 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1566 TYR Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1709 LEU Chi-restraints excluded: chain A residue 1713 HIS Chi-restraints excluded: chain C residue 342 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 66 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 145 optimal weight: 30.0000 chunk 76 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 ASN ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 HIS ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN ** A1545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.074520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.052234 restraints weight = 408465.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.053577 restraints weight = 271385.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.054160 restraints weight = 208400.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.054778 restraints weight = 176761.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.055169 restraints weight = 154304.451| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.7674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 13560 Z= 0.276 Angle : 0.799 9.330 18621 Z= 0.428 Chirality : 0.046 0.826 2169 Planarity : 0.006 0.062 2167 Dihedral : 11.084 160.654 2309 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 27.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.45 % Favored : 94.49 % Rotamer: Outliers : 3.00 % Allowed : 10.36 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.74 (0.21), residues: 1487 helix: 0.11 (0.18), residues: 749 sheet: -1.30 (0.32), residues: 220 loop : -0.77 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 800 TYR 0.033 0.003 TYR A1566 PHE 0.026 0.004 PHE A1760 TRP 0.013 0.002 TRP A1825 HIS 0.013 0.003 HIS A1325 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.28 (13560) covalent geometry : angle 0.79883 / 0.43 (18621) hydrogen bonds : bond 0.06827 / 4.55 ( 704) hydrogen bonds : angle 5.53249 / 4.02 ( 1968) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 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 174 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.669 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: A 306 CYS cc_start: 0.9586 (t) cc_final: 0.9350 (p) REVERT: A 844 GLU cc_start: 0.9511 (OUTLIER) cc_final: 0.9302 (mm-30) REVERT: A 1671 PHE cc_start: 0.8377 (m-10) cc_final: 0.8154 (m-10) outliers start: 40 outliers final: 32 residues processed: 162 average time/residue: 0.2919 time to fit residues: 67.3272 Evaluate side-chains 149 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 771 TYR Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 850 HIS Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1545 HIS Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1572 GLU Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1709 LEU Chi-restraints excluded: chain A residue 1816 ASP Chi-restraints excluded: chain C residue 71 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 152 optimal weight: 20.0000 chunk 18 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 HIS ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.071827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.046243 restraints weight = 278014.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.047877 restraints weight = 175145.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.048755 restraints weight = 128338.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.049670 restraints weight = 105242.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.050141 restraints weight = 91289.843| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.8054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13560 Z= 0.145 Angle : 0.586 7.430 18621 Z= 0.309 Chirality : 0.042 0.784 2169 Planarity : 0.005 0.047 2167 Dihedral : 10.777 161.904 2307 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.48 % Allowed : 13.21 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.06 (0.21), residues: 1487 helix: 0.73 (0.18), residues: 751 sheet: -1.05 (0.33), residues: 216 loop : -0.54 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.017 0.002 TYR A1829 PHE 0.013 0.002 PHE A1839 TRP 0.011 0.001 TRP A 316 HIS 0.009 0.001 HIS A1325 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (13560) covalent geometry : angle 0.58634 / 0.31 (18621) hydrogen bonds : bond 0.04902 / 3.22 ( 704) hydrogen bonds : angle 4.96337 / 3.63 ( 1968) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 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 153 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.567 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: A 233 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8003 (t0) REVERT: A 844 GLU cc_start: 0.9522 (OUTLIER) cc_final: 0.9317 (mm-30) REVERT: A 993 THR cc_start: 0.4771 (OUTLIER) cc_final: 0.4519 (m) outliers start: 33 outliers final: 27 residues processed: 142 average time/residue: 0.2470 time to fit residues: 50.1406 Evaluate side-chains 140 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 850 HIS Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1566 TYR Chi-restraints excluded: chain A residue 1651 LYS Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1670 ARG Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain A residue 1709 LEU Chi-restraints excluded: chain A residue 1713 HIS Chi-restraints excluded: chain A residue 1731 SER Chi-restraints excluded: chain A residue 1832 MET Chi-restraints excluded: chain C residue 342 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 127 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 HIS ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.074247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.053886 restraints weight = 403632.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.054019 restraints weight = 270962.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.054930 restraints weight = 204367.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.055667 restraints weight = 160855.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.055989 restraints weight = 143652.791| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.8758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 13560 Z= 0.183 Angle : 0.605 7.900 18621 Z= 0.322 Chirality : 0.042 0.805 2169 Planarity : 0.005 0.045 2167 Dihedral : 10.844 160.584 2307 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.85 % Allowed : 13.51 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.03 (0.22), residues: 1487 helix: 0.83 (0.18), residues: 754 sheet: -1.10 (0.34), residues: 217 loop : -0.51 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 935 TYR 0.017 0.002 TYR A1829 PHE 0.016 0.002 PHE A1578 TRP 0.007 0.001 TRP A 138 HIS 0.017 0.002 HIS A 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 (13560) covalent geometry : angle 0.60457 / 0.32 (18621) hydrogen bonds : bond 0.05103 / 3.39 ( 704) hydrogen bonds : angle 5.02722 / 3.68 ( 1968) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 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 153 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.514 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 233 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.7774 (t0) REVERT: A 844 GLU cc_start: 0.9522 (OUTLIER) cc_final: 0.9277 (mm-30) outliers start: 38 outliers final: 27 residues processed: 141 average time/residue: 0.2654 time to fit residues: 53.1714 Evaluate side-chains 139 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 895 LYS Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1004 HIS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1651 LYS Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1670 ARG Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain A residue 1709 LEU Chi-restraints excluded: chain A residue 1815 MET Chi-restraints excluded: chain A residue 1832 MET Chi-restraints excluded: chain C residue 342 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 5 optimal weight: 0.6980 chunk 139 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 143 optimal weight: 30.0000 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 301 GLN ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.070984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.048755 restraints weight = 422440.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.049915 restraints weight = 284048.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.050317 restraints weight = 224628.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.051211 restraints weight = 196561.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.051446 restraints weight = 174757.565| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 1.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13560 Z= 0.298 Angle : 0.801 8.531 18621 Z= 0.435 Chirality : 0.047 0.855 2169 Planarity : 0.007 0.072 2167 Dihedral : 12.044 158.740 2307 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 31.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.28 % Allowed : 12.54 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -1.16 (0.21), residues: 1487 helix: -0.20 (0.18), residues: 753 sheet: -1.46 (0.32), residues: 214 loop : -1.08 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 536 TYR 0.036 0.003 TYR A1829 PHE 0.035 0.004 PHE A 836 TRP 0.010 0.002 TRP A 138 HIS 0.023 0.003 HIS A 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.30 (13560) covalent geometry : angle 0.80093 / 0.43 (18621) hydrogen bonds : bond 0.07327 / 4.86 ( 704) hydrogen bonds : angle 5.91323 / 4.30 ( 1968) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 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 164 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 107 time to evaluate : 0.663 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 446 ILE cc_start: 0.8921 (mt) cc_final: 0.8670 (mm) REVERT: A 672 ASN cc_start: 0.8880 (t0) cc_final: 0.8343 (p0) REVERT: A 992 HIS cc_start: 0.8590 (m170) cc_final: 0.8302 (t-90) REVERT: A 1566 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.8161 (m-80) outliers start: 57 outliers final: 47 residues processed: 149 average time/residue: 0.2346 time to fit residues: 49.8476 Evaluate side-chains 145 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 97 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 850 HIS Chi-restraints excluded: chain A residue 895 LYS Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 995 SER Chi-restraints excluded: chain A residue 1004 HIS Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1566 TYR Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1651 LYS Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1670 ARG Chi-restraints excluded: chain A residue 1693 ASP Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain A residue 1709 LEU Chi-restraints excluded: chain A residue 1731 SER Chi-restraints excluded: chain A residue 1761 HIS Chi-restraints excluded: chain A residue 1765 ASP Chi-restraints excluded: chain A residue 1815 MET Chi-restraints excluded: chain A residue 1816 ASP Chi-restraints excluded: chain A residue 1832 MET Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 342 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 45 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 125 optimal weight: 20.0000 chunk 148 optimal weight: 8.9990 chunk 32 optimal weight: 0.0270 chunk 151 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 overall best weight: 2.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 HIS ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.068723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.043578 restraints weight = 288520.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.044841 restraints weight = 188301.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.045721 restraints weight = 142758.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.046152 restraints weight = 118749.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.046722 restraints weight = 103997.263| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 1.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13560 Z= 0.162 Angle : 0.625 7.639 18621 Z= 0.331 Chirality : 0.043 0.797 2169 Planarity : 0.005 0.047 2167 Dihedral : 11.600 159.057 2307 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.00 % Allowed : 14.86 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.56 (0.21), residues: 1487 helix: 0.39 (0.18), residues: 753 sheet: -1.38 (0.34), residues: 212 loop : -0.85 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 935 TYR 0.017 0.002 TYR A1829 PHE 0.012 0.002 PHE A1769 TRP 0.015 0.002 TRP A1380 HIS 0.010 0.002 HIS A1545 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (13560) covalent geometry : angle 0.62545 / 0.33 (18621) hydrogen bonds : bond 0.05243 / 3.47 ( 704) hydrogen bonds : angle 5.33466 / 3.89 ( 1968) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 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 146 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 0.667 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: A 52 LEU cc_start: 0.9766 (tp) cc_final: 0.9557 (mt) REVERT: A 672 ASN cc_start: 0.8828 (t0) cc_final: 0.8328 (p0) REVERT: A 844 GLU cc_start: 0.9593 (OUTLIER) cc_final: 0.9375 (mm-30) REVERT: A 992 HIS cc_start: 0.8585 (m-70) cc_final: 0.8384 (t-90) outliers start: 40 outliers final: 33 residues processed: 138 average time/residue: 0.2564 time to fit residues: 50.4633 Evaluate side-chains 135 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 850 HIS Chi-restraints excluded: chain A residue 895 LYS Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1004 HIS Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1545 HIS Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1651 LYS Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1670 ARG Chi-restraints excluded: chain A residue 1693 ASP Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain A residue 1709 LEU Chi-restraints excluded: chain A residue 1815 MET Chi-restraints excluded: chain A residue 1832 MET Chi-restraints excluded: chain C residue 342 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 18 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 152 optimal weight: 30.0000 chunk 126 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.069371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.044439 restraints weight = 290719.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.045582 restraints weight = 182233.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.046547 restraints weight = 134583.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.047298 restraints weight = 110314.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.047713 restraints weight = 96764.408| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 1.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13560 Z= 0.137 Angle : 0.589 7.733 18621 Z= 0.309 Chirality : 0.042 0.799 2169 Planarity : 0.005 0.045 2167 Dihedral : 11.291 157.093 2307 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.25 % Allowed : 15.77 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 1487 helix: 0.72 (0.18), residues: 760 sheet: -1.27 (0.34), residues: 208 loop : -0.81 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 935 TYR 0.030 0.002 TYR A1748 PHE 0.014 0.002 PHE A1806 TRP 0.012 0.001 TRP A 138 HIS 0.009 0.001 HIS A1325 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (13560) covalent geometry : angle 0.58949 / 0.31 (18621) hydrogen bonds : bond 0.04548 / 3.02 ( 704) hydrogen bonds : angle 5.01603 / 3.67 ( 1968) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 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 136 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.683 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 457 LEU cc_start: 0.9526 (tp) cc_final: 0.9229 (mt) REVERT: A 672 ASN cc_start: 0.8877 (t0) cc_final: 0.8330 (p0) REVERT: A 844 GLU cc_start: 0.9465 (OUTLIER) cc_final: 0.9174 (mm-30) outliers start: 30 outliers final: 28 residues processed: 128 average time/residue: 0.2402 time to fit residues: 43.9746 Evaluate side-chains 134 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 850 HIS Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1004 HIS Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1670 ARG Chi-restraints excluded: chain A residue 1693 ASP Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain A residue 1709 LEU Chi-restraints excluded: chain A residue 1761 HIS Chi-restraints excluded: chain A residue 1815 MET Chi-restraints excluded: chain A residue 1832 MET Chi-restraints excluded: chain C residue 342 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 33 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 672 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 = 0.4076 r_free = 0.4076 target = 0.075854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.055158 restraints weight = 447595.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.056683 restraints weight = 267846.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.057366 restraints weight = 209601.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.057521 restraints weight = 177422.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.057521 restraints weight = 163340.674| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 1.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13560 Z= 0.176 Angle : 0.615 8.099 18621 Z= 0.327 Chirality : 0.042 0.819 2169 Planarity : 0.005 0.045 2167 Dihedral : 11.379 155.127 2307 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.48 % Allowed : 16.14 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.14 (0.22), residues: 1487 helix: 0.80 (0.19), residues: 754 sheet: -1.20 (0.34), residues: 208 loop : -0.78 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 640 TYR 0.026 0.002 TYR A1566 PHE 0.016 0.002 PHE A 836 TRP 0.010 0.002 TRP A 138 HIS 0.011 0.002 HIS A1325 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.18 (13560) covalent geometry : angle 0.61525 / 0.33 (18621) hydrogen bonds : bond 0.04951 / 3.32 ( 704) hydrogen bonds : angle 5.14049 / 3.75 ( 1968) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 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 137 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.738 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 457 LEU cc_start: 0.9539 (tp) cc_final: 0.9250 (mt) REVERT: A 672 ASN cc_start: 0.8771 (t0) cc_final: 0.8290 (p0) REVERT: A 844 GLU cc_start: 0.9542 (OUTLIER) cc_final: 0.9287 (mm-30) outliers start: 33 outliers final: 30 residues processed: 130 average time/residue: 0.2511 time to fit residues: 47.9910 Evaluate side-chains 134 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 92 HIS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 850 HIS Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1004 HIS Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1565 CYS Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1670 ARG Chi-restraints excluded: chain A residue 1693 ASP Chi-restraints excluded: chain A residue 1709 LEU Chi-restraints excluded: chain A residue 1761 HIS Chi-restraints excluded: chain A residue 1815 MET Chi-restraints excluded: chain A residue 1832 MET Chi-restraints excluded: chain C residue 342 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 40.0000 chunk 33 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 150 optimal weight: 20.0000 chunk 67 optimal weight: 0.0670 chunk 52 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 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 = 0.3926 r_free = 0.3926 target = 0.069195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.043887 restraints weight = 289115.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.045252 restraints weight = 188680.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.046180 restraints weight = 141770.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.046615 restraints weight = 117776.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.047234 restraints weight = 103543.241| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 1.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13560 Z= 0.129 Angle : 0.576 7.791 18621 Z= 0.302 Chirality : 0.042 0.802 2169 Planarity : 0.005 0.048 2167 Dihedral : 11.236 154.876 2307 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.33 % Allowed : 16.14 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.10 (0.22), residues: 1487 helix: 1.03 (0.19), residues: 756 sheet: -1.19 (0.35), residues: 203 loop : -0.70 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 935 TYR 0.025 0.002 TYR A1748 PHE 0.016 0.002 PHE A1806 TRP 0.011 0.002 TRP A 138 HIS 0.007 0.001 HIS A1325 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (13560) covalent geometry : angle 0.57633 / 0.30 (18621) hydrogen bonds : bond 0.04284 / 2.87 ( 704) hydrogen bonds : angle 4.89526 / 3.57 ( 1968) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5497.19 seconds wall clock time: 110 minutes 17.64 seconds (6617.64 seconds total)