Starting phenix.real_space_refine on Sun Jun 22 23:29:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zpk_14856/06_2025/7zpk_14856.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zpk_14856/06_2025/7zpk_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zpk_14856/06_2025/7zpk_14856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zpk_14856/06_2025/7zpk_14856.map" model { file = "/net/cci-nas-00/data/ceres_data/7zpk_14856/06_2025/7zpk_14856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zpk_14856/06_2025/7zpk_14856.cif" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 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: 13.26, per 1000 atoms: 0.51 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: 7.08 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 11.45 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: 11.41 Time building geometry restraints manager: 7.83 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: 12046 35.86 - 71.71: 403 71.71 - 107.56: 24 107.56 - 143.42: 1 143.42 - 179.27: 9 Dihedral angle restraints: 12483 sinusoidal: 7329 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 12480 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: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.420 Extract box with map and model: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 65.960 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5672 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 : 15.299 152.539 5496 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.043 0.007 TRP A 316 HIS 0.015 0.003 HIS A1749 PHE 0.033 0.004 PHE C 306 TYR 0.046 0.007 TYR A1695 ARG 0.051 0.006 ARG A 459 Details of bonding type rmsd hydrogen bonds : bond 0.12842 ( 704) hydrogen bonds : angle 5.69925 ( 1968) covalent geometry : bond 0.00360 (13560) covalent geometry : angle 0.80641 (18621) *********************** 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 : 1.784 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 129 VAL cc_start: 0.8393 (t) cc_final: 0.8190 (t) 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: 0.9372 (tp) REVERT: A 637 TYR cc_start: 0.8382 (t80) cc_final: 0.8179 (t80) REVERT: A 1674 LYS cc_start: 0.7797 (mmtt) cc_final: 0.6481 (mmtt) REVERT: A 1683 HIS cc_start: 0.7726 (t-90) cc_final: 0.7396 (t70) 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: 0.6832 time to fit residues: 218.7771 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 : 1.751 ------------------------------------------------------------------------------- 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 131 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 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 = 0.4035 r_free = 0.4035 target = 0.077195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.049750 restraints weight = 269724.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.051393 restraints weight = 172676.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.052593 restraints weight = 127448.104| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13560 Z= 0.230 Angle : 0.724 10.446 18621 Z= 0.380 Chirality : 0.045 0.806 2169 Planarity : 0.006 0.060 2167 Dihedral : 15.586 156.221 2520 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.95 % Allowed : 7.06 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1487 helix: 0.85 (0.18), residues: 749 sheet: -0.65 (0.33), residues: 221 loop : -0.03 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1825 HIS 0.008 0.002 HIS A 335 PHE 0.019 0.002 PHE A 572 TYR 0.023 0.002 TYR A1566 ARG 0.010 0.001 ARG A 640 Details of bonding type rmsd hydrogen bonds : bond 0.06364 ( 704) hydrogen bonds : angle 5.02296 ( 1968) covalent geometry : bond 0.00477 (13560) covalent geometry : angle 0.72421 (18621) *********************** 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 184 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 2.067 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: A 153 TYR cc_start: 0.9678 (m-10) cc_final: 0.9425 (m-10) REVERT: A 306 CYS cc_start: 0.9344 (OUTLIER) cc_final: 0.9093 (p) REVERT: A 471 LEU cc_start: 0.8202 (mt) cc_final: 0.7920 (mt) REVERT: A 562 MET cc_start: 0.5606 (tpp) cc_final: 0.5341 (tpp) REVERT: A 1544 LEU cc_start: 0.8241 (mm) cc_final: 0.8025 (pt) REVERT: A 1683 HIS cc_start: 0.8350 (t-90) cc_final: 0.7775 (t70) REVERT: A 1695 TYR cc_start: 0.8269 (p90) cc_final: 0.7867 (p90) REVERT: A 1764 ASP cc_start: 0.8248 (m-30) cc_final: 0.8007 (m-30) outliers start: 26 outliers final: 21 residues processed: 173 average time/residue: 0.7131 time to fit residues: 171.6639 Evaluate side-chains 153 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 708 LEU 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 1062 HIS 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 1656 LEU 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 59 optimal weight: 0.7980 chunk 139 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 60 optimal weight: 0.4980 chunk 83 optimal weight: 0.9980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 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 = 0.4087 r_free = 0.4087 target = 0.080087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.056899 restraints weight = 390134.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.058518 restraints weight = 250861.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.059302 restraints weight = 187501.991| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13560 Z= 0.144 Angle : 0.564 7.393 18621 Z= 0.297 Chirality : 0.042 0.779 2169 Planarity : 0.005 0.073 2167 Dihedral : 15.404 159.927 2519 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.50 % Allowed : 8.86 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.22), residues: 1487 helix: 1.29 (0.18), residues: 761 sheet: -0.41 (0.36), residues: 207 loop : 0.03 (0.29), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1048 HIS 0.009 0.001 HIS A1062 PHE 0.012 0.001 PHE C 306 TYR 0.014 0.001 TYR A1891 ARG 0.003 0.000 ARG A1892 Details of bonding type rmsd hydrogen bonds : bond 0.04920 ( 704) hydrogen bonds : angle 4.63032 ( 1968) covalent geometry : bond 0.00292 (13560) covalent geometry : angle 0.56433 (18621) *********************** 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 161 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 2.015 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: A 153 TYR cc_start: 0.9681 (m-10) cc_final: 0.9425 (m-10) REVERT: A 176 GLU cc_start: 0.8567 (mm-30) cc_final: 0.7851 (mp0) REVERT: A 1544 LEU cc_start: 0.8233 (mm) cc_final: 0.8003 (pt) REVERT: A 1671 PHE cc_start: 0.8665 (m-10) cc_final: 0.8372 (m-10) REVERT: A 1683 HIS cc_start: 0.8249 (t-90) cc_final: 0.7825 (t70) REVERT: A 1764 ASP cc_start: 0.8473 (m-30) cc_final: 0.8164 (m-30) outliers start: 20 outliers final: 17 residues processed: 153 average time/residue: 0.6833 time to fit residues: 148.1132 Evaluate side-chains 147 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.837 ------------------------------------------------------------------------------- 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 1566 TYR Chi-restraints excluded: chain A residue 1572 GLU Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1713 HIS Chi-restraints excluded: chain A residue 1760 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 41 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A1299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.074750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.049383 restraints weight = 283173.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.050784 restraints weight = 183949.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.051791 restraints weight = 136578.249| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13560 Z= 0.158 Angle : 0.590 11.976 18621 Z= 0.308 Chirality : 0.042 0.791 2169 Planarity : 0.005 0.066 2167 Dihedral : 15.448 161.405 2519 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.28 % Allowed : 10.74 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.22), residues: 1487 helix: 1.36 (0.18), residues: 751 sheet: -0.64 (0.34), residues: 224 loop : 0.09 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1825 HIS 0.007 0.002 HIS A1062 PHE 0.011 0.002 PHE A 72 TYR 0.018 0.002 TYR A1566 ARG 0.008 0.001 ARG A 509 Details of bonding type rmsd hydrogen bonds : bond 0.04767 ( 704) hydrogen bonds : angle 4.62644 ( 1968) covalent geometry : bond 0.00335 (13560) covalent geometry : angle 0.58969 (18621) *********************** 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 149 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 1.879 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: A 153 TYR cc_start: 0.9771 (m-10) cc_final: 0.9568 (m-10) REVERT: A 306 CYS cc_start: 0.9427 (t) cc_final: 0.9199 (p) REVERT: A 844 GLU cc_start: 0.9361 (OUTLIER) cc_final: 0.9111 (mm-30) REVERT: A 1557 ASP cc_start: 0.7698 (m-30) cc_final: 0.7496 (m-30) REVERT: A 1671 PHE cc_start: 0.8455 (m-10) cc_final: 0.8160 (m-10) REVERT: A 1683 HIS cc_start: 0.8219 (t-90) cc_final: 0.7696 (t70) REVERT: A 1695 TYR cc_start: 0.8176 (p90) cc_final: 0.7870 (p90) REVERT: A 1831 MET cc_start: 0.7330 (mmt) cc_final: 0.7013 (mmt) outliers start: 17 outliers final: 13 residues processed: 144 average time/residue: 0.6599 time to fit residues: 131.8609 Evaluate side-chains 136 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 351 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 844 GLU Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1566 TYR Chi-restraints excluded: chain A residue 1572 GLU Chi-restraints excluded: chain A residue 1656 LEU 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 C residue 342 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 144 optimal weight: 0.0980 chunk 68 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 135 optimal weight: 20.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 766 GLN ** 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 = 0.4082 r_free = 0.4082 target = 0.079379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.058208 restraints weight = 388160.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.058919 restraints weight = 257368.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.059437 restraints weight = 185105.614| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13560 Z= 0.103 Angle : 0.518 7.533 18621 Z= 0.267 Chirality : 0.041 0.775 2169 Planarity : 0.004 0.072 2167 Dihedral : 15.320 162.174 2519 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.58 % Allowed : 11.04 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.22), residues: 1487 helix: 1.67 (0.19), residues: 751 sheet: -0.48 (0.35), residues: 221 loop : 0.23 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 316 HIS 0.006 0.001 HIS A 850 PHE 0.011 0.001 PHE C 306 TYR 0.017 0.001 TYR A 876 ARG 0.005 0.000 ARG A1060 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 704) hydrogen bonds : angle 4.34257 ( 1968) covalent geometry : bond 0.00230 (13560) covalent geometry : angle 0.51783 (18621) *********************** 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 145 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 2.099 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: A 153 TYR cc_start: 0.9711 (m-10) cc_final: 0.9491 (m-10) REVERT: A 233 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.7840 (t0) REVERT: A 813 ILE cc_start: 0.8746 (pt) cc_final: 0.8488 (mt) REVERT: A 842 MET cc_start: 0.8624 (mmt) cc_final: 0.8335 (mmt) REVERT: A 897 MET cc_start: 0.8675 (ttm) cc_final: 0.8263 (ttp) REVERT: A 1375 ASP cc_start: 0.9269 (t0) cc_final: 0.9026 (p0) REVERT: A 1671 PHE cc_start: 0.8527 (m-10) cc_final: 0.8151 (m-10) REVERT: A 1683 HIS cc_start: 0.8283 (t-90) cc_final: 0.7693 (t70) REVERT: A 1695 TYR cc_start: 0.8120 (p90) cc_final: 0.7784 (p90) REVERT: A 1831 MET cc_start: 0.7208 (mmt) cc_final: 0.6952 (mmt) outliers start: 21 outliers final: 17 residues processed: 136 average time/residue: 0.6777 time to fit residues: 129.2241 Evaluate side-chains 137 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 233 ASP 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 991 ASP 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 1656 LEU 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 1854 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 109 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 68 optimal weight: 0.5980 chunk 107 optimal weight: 7.9990 chunk 139 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 ASN ** 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 = 0.4002 r_free = 0.4002 target = 0.073207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.048159 restraints weight = 277952.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.049356 restraints weight = 185696.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.050290 restraints weight = 137938.956| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.7039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13560 Z= 0.173 Angle : 0.618 7.942 18621 Z= 0.325 Chirality : 0.043 0.806 2169 Planarity : 0.005 0.069 2167 Dihedral : 15.628 160.340 2519 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.70 % Rotamer: Outliers : 2.25 % Allowed : 10.89 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.22), residues: 1487 helix: 1.28 (0.18), residues: 748 sheet: -0.73 (0.34), residues: 217 loop : -0.16 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1825 HIS 0.008 0.002 HIS A 83 PHE 0.019 0.002 PHE A 537 TYR 0.018 0.002 TYR A1829 ARG 0.005 0.001 ARG C 353 Details of bonding type rmsd hydrogen bonds : bond 0.04971 ( 704) hydrogen bonds : angle 4.66967 ( 1968) covalent geometry : bond 0.00365 (13560) covalent geometry : angle 0.61758 (18621) *********************** 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 163 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 2.058 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: A 233 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.7682 (t0) REVERT: A 306 CYS cc_start: 0.9233 (t) cc_final: 0.9026 (p) REVERT: A 562 MET cc_start: 0.6562 (tpp) cc_final: 0.6238 (mmm) REVERT: A 1557 ASP cc_start: 0.8154 (m-30) cc_final: 0.7755 (m-30) REVERT: A 1560 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6973 (mt-10) REVERT: A 1695 TYR cc_start: 0.8355 (p90) cc_final: 0.8129 (p90) REVERT: A 1738 ILE cc_start: 0.8741 (mm) cc_final: 0.8515 (mm) outliers start: 30 outliers final: 23 residues processed: 150 average time/residue: 0.6800 time to fit residues: 144.1193 Evaluate side-chains 146 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 637 TYR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 850 HIS 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 1572 GLU Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1656 LEU 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 1821 LEU Chi-restraints excluded: chain A residue 1832 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 142 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 HIS ** 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 = 0.4046 r_free = 0.4046 target = 0.077098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.054535 restraints weight = 394672.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.055777 restraints weight = 257962.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.056636 restraints weight = 198350.276| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.7400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13560 Z= 0.115 Angle : 0.537 8.916 18621 Z= 0.279 Chirality : 0.042 0.787 2169 Planarity : 0.004 0.076 2167 Dihedral : 15.532 160.265 2517 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.50 % Allowed : 13.06 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.22), residues: 1487 helix: 1.59 (0.19), residues: 751 sheet: -0.59 (0.35), residues: 221 loop : -0.05 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 316 HIS 0.009 0.001 HIS A1761 PHE 0.011 0.001 PHE A 174 TYR 0.012 0.001 TYR A1829 ARG 0.002 0.000 ARG A1892 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 704) hydrogen bonds : angle 4.41800 ( 1968) covalent geometry : bond 0.00250 (13560) covalent geometry : angle 0.53666 (18621) *********************** 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 146 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 2.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.7941 (t0) REVERT: A 897 MET cc_start: 0.8869 (ttm) cc_final: 0.8451 (ttp) REVERT: A 1695 TYR cc_start: 0.8231 (p90) cc_final: 0.7991 (p90) REVERT: A 1738 ILE cc_start: 0.8921 (mm) cc_final: 0.8714 (mm) outliers start: 20 outliers final: 18 residues processed: 140 average time/residue: 0.6723 time to fit residues: 130.6611 Evaluate side-chains 138 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 708 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 850 HIS Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1566 TYR Chi-restraints excluded: chain A residue 1572 GLU Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain A residue 1709 LEU 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: 7.9990 chunk 50 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 141 optimal weight: 30.0000 chunk 66 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 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 = 0.4003 r_free = 0.4003 target = 0.074365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.052560 restraints weight = 403695.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.053784 restraints weight = 272106.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.054494 restraints weight = 201484.081| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.9009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13560 Z= 0.222 Angle : 0.679 11.875 18621 Z= 0.361 Chirality : 0.044 0.832 2169 Planarity : 0.005 0.068 2167 Dihedral : 15.948 157.484 2517 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.84 % Favored : 95.09 % Rotamer: Outliers : 1.95 % Allowed : 13.59 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1487 helix: 0.89 (0.18), residues: 758 sheet: -0.80 (0.35), residues: 217 loop : -0.39 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A1380 HIS 0.011 0.002 HIS A 83 PHE 0.022 0.003 PHE A 836 TYR 0.027 0.002 TYR A1828 ARG 0.006 0.001 ARG A 935 Details of bonding type rmsd hydrogen bonds : bond 0.05474 ( 704) hydrogen bonds : angle 4.92286 ( 1968) covalent geometry : bond 0.00452 (13560) covalent geometry : angle 0.67859 (18621) *********************** 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 157 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.888 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: A 233 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.7745 (t0) REVERT: A 562 MET cc_start: 0.6890 (tpp) cc_final: 0.6585 (mmm) REVERT: A 842 MET cc_start: 0.9344 (mmt) cc_final: 0.9048 (tpp) REVERT: A 897 MET cc_start: 0.8882 (ttm) cc_final: 0.8527 (ttp) REVERT: A 1560 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7493 (mt-10) REVERT: A 1695 TYR cc_start: 0.8503 (p90) cc_final: 0.8247 (p90) REVERT: A 1738 ILE cc_start: 0.9048 (mm) cc_final: 0.8837 (mm) outliers start: 26 outliers final: 23 residues processed: 149 average time/residue: 0.6915 time to fit residues: 146.2936 Evaluate side-chains 143 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 161 ASN 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 586 LEU Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 843 LEU 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 1066 THR Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1572 GLU Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain A residue 1709 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 48 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 141 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 HIS A1299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.075381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.052584 restraints weight = 395032.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.053635 restraints weight = 254339.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.054282 restraints weight = 187536.899| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.9260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13560 Z= 0.130 Angle : 0.559 8.285 18621 Z= 0.293 Chirality : 0.042 0.799 2169 Planarity : 0.005 0.073 2167 Dihedral : 15.820 157.410 2517 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.95 % Allowed : 14.19 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.22), residues: 1487 helix: 1.31 (0.19), residues: 749 sheet: -0.66 (0.36), residues: 216 loop : -0.22 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1380 HIS 0.008 0.001 HIS A1325 PHE 0.015 0.002 PHE A1374 TYR 0.013 0.001 TYR A1829 ARG 0.003 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 704) hydrogen bonds : angle 4.60097 ( 1968) covalent geometry : bond 0.00280 (13560) covalent geometry : angle 0.55929 (18621) *********************** 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 145 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 2.715 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 233 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.7721 (t0) REVERT: A 450 ARG cc_start: 0.9099 (mtp85) cc_final: 0.8879 (mtm110) REVERT: A 457 LEU cc_start: 0.9254 (tp) cc_final: 0.8969 (mt) REVERT: A 562 MET cc_start: 0.6499 (tpp) cc_final: 0.6134 (mmm) REVERT: A 842 MET cc_start: 0.9252 (mmt) cc_final: 0.8769 (tpp) REVERT: A 897 MET cc_start: 0.8696 (ttm) cc_final: 0.8352 (ttp) REVERT: A 1695 TYR cc_start: 0.8326 (p90) cc_final: 0.8110 (p90) REVERT: A 1738 ILE cc_start: 0.8970 (mm) cc_final: 0.8761 (mm) outliers start: 26 outliers final: 21 residues processed: 134 average time/residue: 0.8388 time to fit residues: 163.2888 Evaluate side-chains 140 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 129 VAL 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 637 TYR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 843 LEU 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 1059 TYR Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1572 GLU Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain A residue 1709 LEU Chi-restraints excluded: chain A residue 1758 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 116 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 52 optimal weight: 0.1980 chunk 118 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 998 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 = 0.3989 r_free = 0.3989 target = 0.072770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.046601 restraints weight = 273982.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.048286 restraints weight = 171096.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.049265 restraints weight = 125489.770| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.9487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13560 Z= 0.106 Angle : 0.535 7.957 18621 Z= 0.276 Chirality : 0.042 0.787 2169 Planarity : 0.004 0.075 2167 Dihedral : 15.567 155.231 2517 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.35 % Allowed : 14.94 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.22), residues: 1487 helix: 1.73 (0.19), residues: 754 sheet: -0.68 (0.36), residues: 218 loop : -0.12 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 316 HIS 0.009 0.001 HIS A1761 PHE 0.013 0.001 PHE A1739 TYR 0.019 0.001 TYR A1566 ARG 0.005 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 704) hydrogen bonds : angle 4.28795 ( 1968) covalent geometry : bond 0.00239 (13560) covalent geometry : angle 0.53488 (18621) ********************** 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 136 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 1.886 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: A 233 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8081 (t0) REVERT: A 325 MET cc_start: 0.5711 (mtp) cc_final: 0.5396 (mtp) REVERT: A 457 LEU cc_start: 0.9355 (tp) cc_final: 0.9031 (mt) REVERT: A 842 MET cc_start: 0.9348 (mmt) cc_final: 0.8811 (tpp) REVERT: A 897 MET cc_start: 0.8957 (ttm) cc_final: 0.8563 (ttp) REVERT: A 1375 ASP cc_start: 0.9551 (t0) cc_final: 0.9331 (p0) REVERT: A 1560 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7084 (mp0) REVERT: A 1695 TYR cc_start: 0.8361 (p90) cc_final: 0.8110 (p90) outliers start: 18 outliers final: 16 residues processed: 132 average time/residue: 0.6312 time to fit residues: 118.1570 Evaluate side-chains 131 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL 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 637 TYR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 850 HIS Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1059 TYR Chi-restraints excluded: chain A residue 1572 GLU Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1709 LEU Chi-restraints excluded: chain C residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 85 optimal weight: 0.0040 chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 overall best weight: 1.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.075269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.053420 restraints weight = 393092.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.054238 restraints weight = 258052.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.055222 restraints weight = 188567.897| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.9844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13560 Z= 0.126 Angle : 0.542 7.833 18621 Z= 0.283 Chirality : 0.041 0.795 2169 Planarity : 0.004 0.073 2167 Dihedral : 15.610 154.202 2517 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.58 % Allowed : 15.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.22), residues: 1487 helix: 1.66 (0.19), residues: 761 sheet: -0.61 (0.36), residues: 210 loop : -0.12 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1825 HIS 0.008 0.001 HIS A1761 PHE 0.016 0.002 PHE A1739 TYR 0.016 0.001 TYR A1828 ARG 0.005 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 704) hydrogen bonds : angle 4.35667 ( 1968) covalent geometry : bond 0.00268 (13560) covalent geometry : angle 0.54185 (18621) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10821.50 seconds wall clock time: 188 minutes 10.18 seconds (11290.18 seconds total)