Starting phenix.real_space_refine on Mon Aug 25 08:18:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zpk_14856/08_2025/7zpk_14856.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zpk_14856/08_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_14856/08_2025/7zpk_14856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zpk_14856/08_2025/7zpk_14856.map" model { file = "/net/cci-nas-00/data/ceres_data/7zpk_14856/08_2025/7zpk_14856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zpk_14856/08_2025/7zpk_14856.cif" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 55 5.49 5 S 70 5.16 5 C 8185 2.51 5 N 2263 2.21 5 O 2602 1.98 5 H 12760 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25935 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 20620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1280, 20620 Classifications: {'peptide': 1280} Link IDs: {'PTRANS': 76, 'TRANS': 1203} Chain breaks: 9 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1763 Classifications: {'RNA': 55} Modifications used: {'3*END': 1, 'rna3p_pur': 28, 'rna3p_pyr': 27} Link IDs: {'rna3p': 54} Chain breaks: 1 Chain: "C" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3552 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 221} Chain breaks: 2 Time building chain proxies: 3.52, per 1000 atoms: 0.14 Number of scatterers: 25935 At special positions: 0 Unit cell: (97.695, 123.58, 162.825, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 70 16.00 P 55 15.00 O 2602 8.00 N 2263 7.00 C 8185 6.00 H 12760 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 637.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 3.67 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: 5.84 Time building geometry restraints manager: 2.67 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: 4.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.880 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.130 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.21), residues: 1487 helix: 0.55 (0.17), residues: 738 sheet: -0.44 (0.35), residues: 201 loop : -0.32 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.051 0.006 ARG A 459 TYR 0.046 0.007 TYR A1695 PHE 0.033 0.004 PHE C 306 TRP 0.043 0.007 TRP A 316 HIS 0.015 0.003 HIS A1749 Details of bonding type rmsd covalent geometry : bond 0.00360 (13560) covalent geometry : angle 0.80641 (18621) hydrogen bonds : bond 0.12842 ( 704) hydrogen bonds : angle 5.69925 ( 1968) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 223 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8242 (mm) cc_final: 0.7934 (mm) REVERT: A 381 LEU cc_start: 0.9665 (mt) cc_final: 0.9367 (tp) REVERT: A 637 TYR cc_start: 0.8382 (t80) cc_final: 0.8179 (t80) REVERT: A 813 ILE cc_start: 0.6817 (pt) cc_final: 0.6603 (mt) REVERT: A 1674 LYS cc_start: 0.7797 (mmtt) cc_final: 0.6298 (mmtt) REVERT: A 1764 ASP cc_start: 0.7695 (m-30) cc_final: 0.7436 (m-30) outliers start: 9 outliers final: 3 residues processed: 231 average time/residue: 0.2877 time to fit residues: 90.9143 Evaluate side-chains 162 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 159 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 364 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.077972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.054180 restraints weight = 401202.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.055781 restraints weight = 265469.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.056529 restraints weight = 197985.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.057245 restraints weight = 165951.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.057248 restraints weight = 141044.029| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 13560 Z= 0.341 Angle : 0.825 8.383 18621 Z= 0.447 Chirality : 0.046 0.770 2169 Planarity : 0.007 0.075 2167 Dihedral : 15.796 155.862 2520 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.03 % Allowed : 7.36 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.21), residues: 1487 helix: 0.32 (0.18), residues: 752 sheet: -0.91 (0.33), residues: 218 loop : -0.31 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 640 TYR 0.032 0.003 TYR A1566 PHE 0.023 0.003 PHE A 98 TRP 0.019 0.003 TRP A1825 HIS 0.011 0.002 HIS A1325 Details of bonding type rmsd covalent geometry : bond 0.00626 (13560) covalent geometry : angle 0.82526 (18621) hydrogen bonds : bond 0.07506 ( 704) hydrogen bonds : angle 5.47010 ( 1968) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.501 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: A 306 CYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8982 (p) REVERT: A 471 LEU cc_start: 0.8295 (mt) cc_final: 0.8045 (mt) REVERT: A 562 MET cc_start: 0.5914 (tpp) cc_final: 0.5614 (tpp) REVERT: A 565 ASP cc_start: 0.9438 (OUTLIER) cc_final: 0.8913 (t0) REVERT: A 1557 ASP cc_start: 0.7707 (m-30) cc_final: 0.7378 (m-30) REVERT: A 1560 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6647 (mt-10) REVERT: A 1683 HIS cc_start: 0.8222 (t-90) cc_final: 0.7529 (t70) REVERT: A 1695 TYR cc_start: 0.8376 (p90) cc_final: 0.8014 (p90) REVERT: A 1764 ASP cc_start: 0.8254 (m-30) cc_final: 0.7863 (m-30) outliers start: 27 outliers final: 20 residues processed: 163 average time/residue: 0.2720 time to fit residues: 62.3375 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 : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 771 TYR Chi-restraints excluded: chain A residue 850 HIS Chi-restraints excluded: chain A residue 886 ASP Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 1566 TYR Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1713 HIS Chi-restraints excluded: chain A residue 1731 SER Chi-restraints excluded: chain A residue 1760 PHE Chi-restraints excluded: chain A residue 1772 GLU Chi-restraints excluded: chain A residue 1821 LEU Chi-restraints excluded: chain C residue 342 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 71 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 141 optimal weight: 20.0000 chunk 118 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN A1305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.079930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.055990 restraints weight = 386866.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.057784 restraints weight = 250590.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.058902 restraints weight = 185785.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.059376 restraints weight = 153770.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.060139 restraints weight = 139901.541| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13560 Z= 0.115 Angle : 0.556 7.622 18621 Z= 0.289 Chirality : 0.042 0.789 2169 Planarity : 0.005 0.059 2167 Dihedral : 15.479 159.919 2519 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.43 % Allowed : 9.38 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.22), residues: 1487 helix: 1.09 (0.18), residues: 758 sheet: -0.51 (0.35), residues: 207 loop : -0.05 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 509 TYR 0.016 0.001 TYR A1676 PHE 0.012 0.002 PHE A1660 TRP 0.010 0.001 TRP A 316 HIS 0.008 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00251 (13560) covalent geometry : angle 0.55633 (18621) hydrogen bonds : bond 0.04919 ( 704) hydrogen bonds : angle 4.69611 ( 1968) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.433 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: A 153 TYR cc_start: 0.9370 (m-10) cc_final: 0.9159 (m-10) REVERT: A 176 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7471 (mp0) REVERT: A 844 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8455 (mm-30) REVERT: A 1557 ASP cc_start: 0.7573 (m-30) cc_final: 0.7354 (m-30) REVERT: A 1683 HIS cc_start: 0.8024 (t-90) cc_final: 0.7375 (t70) REVERT: A 1695 TYR cc_start: 0.8145 (p90) cc_final: 0.7772 (p90) outliers start: 19 outliers final: 15 residues processed: 153 average time/residue: 0.2571 time to fit residues: 54.8348 Evaluate side-chains 144 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 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 932 ILE Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1566 TYR Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1709 LEU Chi-restraints excluded: chain A residue 1713 HIS Chi-restraints excluded: chain A residue 1760 PHE Chi-restraints excluded: chain C residue 342 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 66 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 145 optimal weight: 50.0000 chunk 76 optimal weight: 0.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN ** A1545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.075637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.053484 restraints weight = 404006.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.054172 restraints weight = 267285.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.055200 restraints weight = 200371.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.055685 restraints weight = 166589.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.056299 restraints weight = 148866.712| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.6732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13560 Z= 0.230 Angle : 0.721 9.996 18621 Z= 0.382 Chirality : 0.045 0.814 2169 Planarity : 0.006 0.062 2167 Dihedral : 15.901 161.257 2518 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.84 % Favored : 95.09 % Rotamer: Outliers : 2.63 % Allowed : 10.44 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.21), residues: 1487 helix: 0.39 (0.18), residues: 752 sheet: -1.09 (0.32), residues: 220 loop : -0.57 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A1060 TYR 0.029 0.003 TYR A1566 PHE 0.033 0.003 PHE A1671 TRP 0.014 0.002 TRP A1825 HIS 0.023 0.003 HIS A1325 Details of bonding type rmsd covalent geometry : bond 0.00471 (13560) covalent geometry : angle 0.72052 (18621) hydrogen bonds : bond 0.06299 ( 704) hydrogen bonds : angle 5.22169 ( 1968) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 CYS cc_start: 0.9171 (t) cc_final: 0.8950 (p) REVERT: A 1544 LEU cc_start: 0.8781 (pt) cc_final: 0.8488 (mm) REVERT: A 1560 GLU cc_start: 0.7530 (mt-10) cc_final: 0.6815 (mt-10) outliers start: 35 outliers final: 30 residues processed: 150 average time/residue: 0.2720 time to fit residues: 57.1042 Evaluate side-chains 143 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 161 ASN Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 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 838 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 850 HIS Chi-restraints excluded: chain A residue 886 ASP Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1566 TYR Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1651 LYS Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1709 LEU Chi-restraints excluded: chain A residue 1816 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 180 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 152 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.075996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.054090 restraints weight = 394909.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.054996 restraints weight = 268201.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.055792 restraints weight = 200452.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.056539 restraints weight = 167106.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.056792 restraints weight = 146274.939| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.7412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13560 Z= 0.149 Angle : 0.583 7.422 18621 Z= 0.306 Chirality : 0.042 0.782 2169 Planarity : 0.005 0.078 2167 Dihedral : 15.764 162.348 2516 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.03 % Allowed : 12.91 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.21), residues: 1487 helix: 0.88 (0.18), residues: 754 sheet: -0.96 (0.33), residues: 216 loop : -0.39 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1901 TYR 0.022 0.001 TYR A1708 PHE 0.014 0.002 PHE A1374 TRP 0.010 0.001 TRP A 316 HIS 0.009 0.001 HIS A1325 Details of bonding type rmsd covalent geometry : bond 0.00312 (13560) covalent geometry : angle 0.58274 (18621) hydrogen bonds : bond 0.04768 ( 704) hydrogen bonds : angle 4.80907 ( 1968) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8105 (mm) REVERT: A 844 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8788 (mm-30) REVERT: A 1560 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6807 (mt-10) outliers start: 27 outliers final: 21 residues processed: 132 average time/residue: 0.2783 time to fit residues: 51.4345 Evaluate side-chains 134 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 164 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 850 HIS Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1709 LEU Chi-restraints excluded: chain A residue 1713 HIS Chi-restraints excluded: chain A residue 1832 MET Chi-restraints excluded: chain A residue 1854 MET Chi-restraints excluded: chain C residue 342 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 127 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1761 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.070581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.045487 restraints weight = 288091.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.047031 restraints weight = 181691.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.047909 restraints weight = 134051.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.048687 restraints weight = 110627.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.049177 restraints weight = 97973.859| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.8484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13560 Z= 0.189 Angle : 0.627 8.063 18621 Z= 0.332 Chirality : 0.043 0.811 2169 Planarity : 0.005 0.070 2167 Dihedral : 15.821 160.216 2516 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.63 % Allowed : 12.84 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.22), residues: 1487 helix: 0.88 (0.18), residues: 753 sheet: -1.04 (0.33), residues: 224 loop : -0.42 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1901 TYR 0.035 0.002 TYR A1566 PHE 0.019 0.002 PHE A 537 TRP 0.008 0.002 TRP A1825 HIS 0.009 0.001 HIS A1325 Details of bonding type rmsd covalent geometry : bond 0.00396 (13560) covalent geometry : angle 0.62738 (18621) hydrogen bonds : bond 0.05092 ( 704) hydrogen bonds : angle 4.92422 ( 1968) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8290 (mm) REVERT: A 233 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.7616 (t0) REVERT: A 446 ILE cc_start: 0.8724 (mt) cc_final: 0.8517 (mp) REVERT: A 844 GLU cc_start: 0.9275 (OUTLIER) cc_final: 0.8982 (mm-30) REVERT: A 993 THR cc_start: 0.3052 (OUTLIER) cc_final: 0.2821 (m) REVERT: A 1316 GLU cc_start: 0.8522 (tt0) cc_final: 0.8078 (tt0) REVERT: A 1560 GLU cc_start: 0.7609 (mt-10) cc_final: 0.6931 (mt-10) outliers start: 35 outliers final: 27 residues processed: 143 average time/residue: 0.2724 time to fit residues: 54.3924 Evaluate side-chains 145 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 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 537 PHE Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 660 ASP 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 844 GLU Chi-restraints excluded: chain A residue 850 HIS Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1670 ARG Chi-restraints excluded: chain A residue 1709 LEU Chi-restraints excluded: chain A residue 1713 HIS 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 5 optimal weight: 0.5980 chunk 139 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 143 optimal weight: 30.0000 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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 850 HIS ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN A1353 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.069309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.045170 restraints weight = 287424.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.046222 restraints weight = 185324.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.047167 restraints weight = 132541.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.047567 restraints weight = 107681.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.047567 restraints weight = 94461.062| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.9925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13560 Z= 0.212 Angle : 0.651 7.888 18621 Z= 0.350 Chirality : 0.044 0.808 2169 Planarity : 0.006 0.076 2167 Dihedral : 16.099 159.104 2516 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.00 % Allowed : 13.06 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.22), residues: 1487 helix: 0.66 (0.18), residues: 762 sheet: -1.07 (0.34), residues: 211 loop : -0.57 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 263 TYR 0.026 0.002 TYR A1566 PHE 0.017 0.002 PHE A1322 TRP 0.011 0.002 TRP A 138 HIS 0.010 0.002 HIS A1325 Details of bonding type rmsd covalent geometry : bond 0.00432 (13560) covalent geometry : angle 0.65070 (18621) hydrogen bonds : bond 0.05356 ( 704) hydrogen bonds : angle 5.11843 ( 1968) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8651 (mm) REVERT: A 457 LEU cc_start: 0.9458 (tp) cc_final: 0.9140 (mt) REVERT: A 562 MET cc_start: 0.7165 (tpp) cc_final: 0.6890 (mmm) REVERT: A 672 ASN cc_start: 0.8608 (t0) cc_final: 0.7964 (p0) REVERT: A 844 GLU cc_start: 0.9419 (OUTLIER) cc_final: 0.9143 (mm-30) REVERT: A 1560 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7215 (mt-10) REVERT: A 1813 ILE cc_start: 0.8213 (mm) cc_final: 0.7882 (mm) outliers start: 40 outliers final: 32 residues processed: 146 average time/residue: 0.2773 time to fit residues: 56.7202 Evaluate side-chains 141 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 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 565 ASP Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 850 HIS Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1004 HIS Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1545 HIS Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1670 ARG Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain A residue 1709 LEU Chi-restraints excluded: chain A residue 1765 ASP Chi-restraints excluded: chain A residue 1832 MET 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: 9.9990 chunk 69 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 chunk 148 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 992 HIS ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.067741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.043432 restraints weight = 289171.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.044689 restraints weight = 184405.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.045320 restraints weight = 135861.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.046016 restraints weight = 115242.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.046423 restraints weight = 101399.052| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 1.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13560 Z= 0.259 Angle : 0.693 8.246 18621 Z= 0.376 Chirality : 0.044 0.830 2169 Planarity : 0.006 0.066 2167 Dihedral : 16.341 157.548 2516 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.12 % Favored : 93.81 % Rotamer: Outliers : 3.15 % Allowed : 14.26 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.21), residues: 1487 helix: 0.27 (0.18), residues: 756 sheet: -1.36 (0.33), residues: 219 loop : -0.81 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 848 TYR 0.040 0.003 TYR A1566 PHE 0.019 0.003 PHE A 836 TRP 0.009 0.002 TRP A1825 HIS 0.032 0.002 HIS A 850 Details of bonding type rmsd covalent geometry : bond 0.00511 (13560) covalent geometry : angle 0.69273 (18621) hydrogen bonds : bond 0.06200 ( 704) hydrogen bonds : angle 5.47746 ( 1968) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 102 time to evaluate : 0.486 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 562 MET cc_start: 0.7302 (tpp) cc_final: 0.6986 (mmm) REVERT: A 672 ASN cc_start: 0.8794 (t0) cc_final: 0.8227 (p0) REVERT: A 1296 LEU cc_start: 0.8543 (mt) cc_final: 0.8167 (pp) REVERT: A 1560 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7407 (mt-10) outliers start: 42 outliers final: 38 residues processed: 134 average time/residue: 0.2506 time to fit residues: 47.4804 Evaluate side-chains 137 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 850 HIS Chi-restraints excluded: chain A residue 895 LYS Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1004 HIS Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1670 ARG Chi-restraints excluded: chain A residue 1693 ASP Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain A residue 1709 LEU Chi-restraints excluded: chain A residue 1765 ASP Chi-restraints excluded: chain A residue 1832 MET Chi-restraints excluded: chain C residue 342 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 18 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 152 optimal weight: 20.0000 chunk 126 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 GLN ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1353 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.067380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.042740 restraints weight = 298902.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.043994 restraints weight = 192352.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.044769 restraints weight = 145323.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.045418 restraints weight = 122062.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.045764 restraints weight = 108658.474| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 1.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 13560 Z= 0.235 Angle : 0.688 11.541 18621 Z= 0.371 Chirality : 0.044 0.804 2169 Planarity : 0.006 0.066 2167 Dihedral : 16.500 155.717 2516 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.30 % Allowed : 14.56 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.21), residues: 1487 helix: 0.26 (0.18), residues: 757 sheet: -1.22 (0.34), residues: 212 loop : -0.95 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 353 TYR 0.026 0.002 TYR A1566 PHE 0.042 0.003 PHE A1839 TRP 0.013 0.002 TRP A 138 HIS 0.025 0.002 HIS A 850 Details of bonding type rmsd covalent geometry : bond 0.00470 (13560) covalent geometry : angle 0.68778 (18621) hydrogen bonds : bond 0.05646 ( 704) hydrogen bonds : angle 5.46111 ( 1968) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 104 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8944 (mm) REVERT: A 562 MET cc_start: 0.7528 (tpp) cc_final: 0.7232 (mmm) REVERT: A 672 ASN cc_start: 0.8963 (t0) cc_final: 0.8447 (p0) REVERT: A 1560 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7459 (mt-10) outliers start: 44 outliers final: 41 residues processed: 138 average time/residue: 0.2431 time to fit residues: 48.1881 Evaluate side-chains 140 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 98 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 171 LEU 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 384 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 850 HIS Chi-restraints excluded: chain A residue 895 LYS Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1004 HIS Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1353 ASN Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1670 ARG Chi-restraints excluded: chain A residue 1693 ASP Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain A residue 1709 LEU Chi-restraints excluded: chain A residue 1731 SER Chi-restraints excluded: chain A residue 1772 GLU Chi-restraints excluded: chain A residue 1832 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 342 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 33 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 143 optimal weight: 30.0000 chunk 19 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.067623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.043325 restraints weight = 278770.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.044499 restraints weight = 179957.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.045333 restraints weight = 136308.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.045741 restraints weight = 114301.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.046176 restraints weight = 100310.448| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 1.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.176 13560 Z= 0.237 Angle : 0.867 59.185 18621 Z= 0.501 Chirality : 0.044 0.803 2169 Planarity : 0.006 0.066 2167 Dihedral : 16.500 155.705 2516 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.08 % Allowed : 15.54 % Favored : 81.38 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.21), residues: 1487 helix: 0.25 (0.18), residues: 757 sheet: -1.23 (0.34), residues: 212 loop : -0.95 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 353 TYR 0.025 0.002 TYR A1566 PHE 0.018 0.002 PHE A1322 TRP 0.012 0.002 TRP A 138 HIS 0.025 0.002 HIS A 850 Details of bonding type rmsd covalent geometry : bond 0.00486 (13560) covalent geometry : angle 0.86701 (18621) hydrogen bonds : bond 0.05634 ( 704) hydrogen bonds : angle 5.44477 ( 1968) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 99 time to evaluate : 0.564 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 171 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8958 (mm) REVERT: A 562 MET cc_start: 0.7513 (tpp) cc_final: 0.7218 (mmm) REVERT: A 672 ASN cc_start: 0.8961 (t0) cc_final: 0.8450 (p0) REVERT: A 1560 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7408 (mt-10) outliers start: 41 outliers final: 40 residues processed: 131 average time/residue: 0.2470 time to fit residues: 46.6952 Evaluate side-chains 139 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 171 LEU 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 384 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 850 HIS Chi-restraints excluded: chain A residue 895 LYS Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1004 HIS Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1670 ARG Chi-restraints excluded: chain A residue 1693 ASP Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain A residue 1709 LEU Chi-restraints excluded: chain A residue 1731 SER Chi-restraints excluded: chain A residue 1772 GLU Chi-restraints excluded: chain A residue 1832 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 342 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 40.0000 chunk 33 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 67 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.067681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.043278 restraints weight = 302192.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.044141 restraints weight = 198699.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.044997 restraints weight = 148962.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.045364 restraints weight = 123942.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.046003 restraints weight = 110044.356| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 1.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.176 13560 Z= 0.237 Angle : 0.867 59.185 18621 Z= 0.501 Chirality : 0.044 0.803 2169 Planarity : 0.006 0.066 2167 Dihedral : 16.500 155.705 2516 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.08 % Allowed : 15.54 % Favored : 81.38 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.21), residues: 1487 helix: 0.25 (0.18), residues: 757 sheet: -1.23 (0.34), residues: 212 loop : -0.95 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 353 TYR 0.025 0.002 TYR A1566 PHE 0.018 0.002 PHE A1322 TRP 0.012 0.002 TRP A 138 HIS 0.025 0.002 HIS A 850 Details of bonding type rmsd covalent geometry : bond 0.00486 (13560) covalent geometry : angle 0.86701 (18621) hydrogen bonds : bond 0.05634 ( 704) hydrogen bonds : angle 5.44477 ( 1968) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5540.23 seconds wall clock time: 94 minutes 55.98 seconds (5695.98 seconds total)