Starting phenix.real_space_refine on Wed Dec 13 19:00:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpk_14856/12_2023/7zpk_14856.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpk_14856/12_2023/7zpk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpk_14856/12_2023/7zpk_14856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpk_14856/12_2023/7zpk_14856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpk_14856/12_2023/7zpk_14856.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpk_14856/12_2023/7zpk_14856.pdb" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 55 5.49 5 S 70 5.16 5 C 8185 2.51 5 N 2263 2.21 5 O 2602 1.98 5 H 12760 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 25935 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 20620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1280, 20620 Classifications: {'peptide': 1280} Link IDs: {'PTRANS': 76, 'TRANS': 1203} Chain breaks: 9 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1763 Classifications: {'RNA': 55} Modifications used: {'3*END': 1, 'rna3p_pur': 28, 'rna3p_pyr': 27} Link IDs: {'rna3p': 54} Chain breaks: 1 Chain: "C" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3552 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 221} Chain breaks: 2 Time building chain proxies: 11.55, per 1000 atoms: 0.45 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 - 3.50 Amino acid : False - 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: 22.11 Conformation dependent library (CDL) restraints added in 2.5 seconds 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2888 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 12 sheets defined 53.5% alpha, 13.9% beta 18 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 13.22 Creating SS restraints... Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.823A pdb=" N ALA A 93 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.865A pdb=" N GLN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 162 Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 184 through 196 removed outlier: 4.283A pdb=" N GLU A 188 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 231 removed outlier: 5.021A pdb=" N GLU A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 265 through 284 Processing helix chain 'A' and resid 294 through 314 Processing helix chain 'A' and resid 314 through 334 removed outlier: 3.803A pdb=" N LYS A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 361 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.609A pdb=" N LYS A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 468 Processing helix chain 'A' and resid 498 through 510 removed outlier: 3.564A pdb=" N GLU A 502 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 519 through 524 Processing helix chain 'A' and resid 542 through 551 Processing helix chain 'A' and resid 565 through 592 removed outlier: 4.046A pdb=" N LYS A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER A 571 " --> pdb=" O ASP A 567 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU A 574 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 641 removed outlier: 4.242A pdb=" N GLY A 632 " --> pdb=" O ASN A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 706 removed outlier: 3.591A pdb=" N LYS A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 859 Processing helix chain 'A' and resid 893 through 902 Processing helix chain 'A' and resid 967 through 976 Processing helix chain 'A' and resid 1044 through 1053 removed outlier: 4.041A pdb=" N CYS A1053 " --> pdb=" O ARG A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1076 Processing helix chain 'A' and resid 1293 through 1302 Processing helix chain 'A' and resid 1303 through 1307 Processing helix chain 'A' and resid 1313 through 1335 Processing helix chain 'A' and resid 1339 through 1352 Processing helix chain 'A' and resid 1352 through 1363 Processing helix chain 'A' and resid 1364 through 1368 Processing helix chain 'A' and resid 1552 through 1583 removed outlier: 7.893A pdb=" N GLU A1572 " --> pdb=" O THR A1568 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ARG A1573 " --> pdb=" O SER A1569 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA A1574 " --> pdb=" O CYS A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1648 through 1657 Processing helix chain 'A' and resid 1660 through 1668 removed outlier: 3.616A pdb=" N LYS A1666 " --> pdb=" O THR A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1674 through 1682 removed outlier: 3.758A pdb=" N LEU A1678 " --> pdb=" O LYS A1674 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1716 removed outlier: 3.622A pdb=" N PHE A1700 " --> pdb=" O GLN A1696 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A1701 " --> pdb=" O ARG A1697 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A1704 " --> pdb=" O PHE A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1735 Processing helix chain 'A' and resid 1735 through 1746 Processing helix chain 'A' and resid 1747 through 1752 removed outlier: 4.011A pdb=" N TYR A1751 " --> pdb=" O ASP A1747 " (cutoff:3.500A) Processing helix chain 'A' and resid 1756 through 1772 removed outlier: 3.724A pdb=" N LYS A1768 " --> pdb=" O ASP A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1799 through 1817 removed outlier: 3.970A pdb=" N GLY A1803 " --> pdb=" O PRO A1799 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1842 Proline residue: A1830 - end of helix Proline residue: A1834 - end of helix removed outlier: 3.695A pdb=" N LYS A1838 " --> pdb=" O PRO A1834 " (cutoff:3.500A) Processing helix chain 'A' and resid 1846 through 1855 Processing helix chain 'A' and resid 1890 through 1910 Processing helix chain 'C' and resid 18 through 26 Processing helix chain 'C' and resid 30 through 42 Processing helix chain 'C' and resid 79 through 95 Processing helix chain 'C' and resid 158 through 170 Processing helix chain 'C' and resid 185 through 189 removed outlier: 4.159A pdb=" N LYS C 189 " --> pdb=" O ALA C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 225 Processing helix chain 'C' and resid 292 through 304 Processing helix chain 'C' and resid 342 through 364 Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.931A pdb=" N THR A 151 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR A 96 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N MET A 150 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N PHE A 98 " --> pdb=" O MET A 150 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ARG A 95 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A 171 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A 175 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR A 60 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR A 206 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL A 62 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE A 61 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 251 through 256 removed outlier: 6.094A pdb=" N CYS A 251 " --> pdb=" O TYR A 560 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N MET A 562 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE A 253 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ALA A 564 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL A 255 " --> pdb=" O ALA A 564 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE A 445 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN A 477 " --> pdb=" O ILE A 517 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 652 through 656 Processing sheet with id=AA4, first strand: chain 'A' and resid 746 through 750 removed outlier: 3.731A pdb=" N GLN A 747 " --> pdb=" O ILE A1550 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 816 through 820 removed outlier: 3.692A pdb=" N PHE A 816 " --> pdb=" O ILE A 827 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLU A 824 " --> pdb=" O THR A 778 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 778 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 832 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU A 770 " --> pdb=" O LYS A 832 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER A 834 " --> pdb=" O CYS A 768 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS A 768 " --> pdb=" O SER A 834 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N PHE A 802 " --> pdb=" O ILE A 773 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR A 889 " --> pdb=" O VAL A 884 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 865 through 867 Processing sheet with id=AA7, first strand: chain 'A' and resid 987 through 992 removed outlier: 3.502A pdb=" N LEU A 987 " --> pdb=" O TYR A 951 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP A 949 " --> pdb=" O ASP A 989 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP A 991 " --> pdb=" O VAL A 947 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N VAL A 947 " --> pdb=" O ASP A 991 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1859 through 1861 Processing sheet with id=AA9, first strand: chain 'A' and resid 1859 through 1861 Processing sheet with id=AB1, first strand: chain 'C' and resid 47 through 56 removed outlier: 5.716A pdb=" N TYR C 48 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N THR C 67 " --> pdb=" O TYR C 48 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU C 50 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG C 65 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN C 56 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 176 through 183 removed outlier: 5.657A pdb=" N TYR C 177 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ARG C 196 " --> pdb=" O TYR C 177 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL C 179 " --> pdb=" O THR C 194 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR C 194 " --> pdb=" O VAL C 179 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 308 through 312 662 hydrogen bonds defined for protein. 1896 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 11.26 Time building geometry restraints manager: 22.71 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: 73.14 - 85.31: 6 85.31 - 97.48: 1 97.48 - 109.64: 19124 109.64 - 121.81: 23964 121.81 - 133.97: 4594 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: 11827 35.86 - 71.71: 296 71.71 - 107.56: 24 107.56 - 143.42: 1 143.42 - 179.27: 9 Dihedral angle restraints: 12157 sinusoidal: 7003 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 12154 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 1.850 nonbonded pdb=" H LYS A 868 " pdb=" O GLY A1384 " model vdw 1.603 1.850 nonbonded pdb=" HG1 THR A1867 " pdb=" OD1 ASP A1869 " model vdw 1.612 1.850 nonbonded pdb=" HG SER A 915 " pdb=" OE1 GLU A 917 " model vdw 1.613 1.850 nonbonded pdb=" O LEU A1678 " pdb=" HG1 THR A1682 " model vdw 1.622 1.850 ... (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 ========== 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.350 Extract box with map and model: 12.780 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 95.340 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.720 ------------------------------------------------------------------------------- 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= 0.237 Angle : 0.806 10.438 18621 Z= 0.458 Chirality : 0.051 0.818 2169 Planarity : 0.015 0.212 2167 Dihedral : 14.874 152.539 5432 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.68 % Allowed : 3.08 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1487 helix: 0.55 (0.17), residues: 738 sheet: -0.44 (0.35), residues: 201 loop : -0.32 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.007 TRP A 316 HIS 0.015 0.003 HIS A1749 PHE 0.033 0.004 PHE C 306 TYR 0.046 0.007 TYR A1695 ARG 0.051 0.006 ARG A 459 *********************** 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 fitting. rotamer outliers: 9 poor density : 223 time to evaluate : 1.961 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 outliers start: 9 outliers final: 3 residues processed: 231 average time/residue: 0.6857 time to fit residues: 221.4328 Evaluate side-chains 158 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 1.948 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.2869 time to fit residues: 4.0582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 0.0010 chunk 122 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 overall best weight: 2.3790 ------------------------------------------------------------------------------- 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** A1062 HIS ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6036 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13560 Z= 0.224 Angle : 0.615 8.218 18621 Z= 0.319 Chirality : 0.042 0.774 2169 Planarity : 0.005 0.080 2167 Dihedral : 14.441 156.425 2452 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.65 % Allowed : 7.58 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1487 helix: 1.25 (0.18), residues: 747 sheet: -0.32 (0.34), residues: 205 loop : 0.05 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 138 HIS 0.007 0.001 HIS A 335 PHE 0.014 0.002 PHE A 572 TYR 0.018 0.002 TYR A1566 ARG 0.021 0.001 ARG A 509 *********************** 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 180 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 158 time to evaluate : 2.206 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 outliers start: 22 outliers final: 18 residues processed: 170 average time/residue: 0.7100 time to fit residues: 165.6560 Evaluate side-chains 155 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 1.984 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.3287 time to fit residues: 12.8971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 HIS ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1041 HIS A1299 GLN ** A1576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1683 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.6681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.210 13560 Z= 0.542 Angle : 0.954 11.309 18621 Z= 0.513 Chirality : 0.050 0.797 2169 Planarity : 0.008 0.108 2167 Dihedral : 15.454 161.957 2452 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 41.16 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.38 % Favored : 94.35 % Rotamer: Outliers : 2.25 % Allowed : 10.74 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.20), residues: 1487 helix: -0.43 (0.17), residues: 741 sheet: -0.98 (0.34), residues: 197 loop : -0.89 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.005 TRP A1048 HIS 0.016 0.003 HIS A1761 PHE 0.036 0.004 PHE A 98 TYR 0.038 0.004 TYR A1748 ARG 0.012 0.001 ARG A1314 *********************** 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 170 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 140 time to evaluate : 2.124 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 outliers start: 30 outliers final: 24 residues processed: 163 average time/residue: 0.6870 time to fit residues: 154.5458 Evaluate side-chains 139 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 1.982 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 24 outliers final: 1 residues processed: 24 average time/residue: 0.3536 time to fit residues: 16.7487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 50.0000 chunk 106 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 20.0000 chunk 150 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** A1299 GLN ** A1576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.6750 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= 0.189 Angle : 0.592 7.360 18621 Z= 0.311 Chirality : 0.042 0.776 2169 Planarity : 0.005 0.065 2167 Dihedral : 14.950 161.760 2452 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.90 % Allowed : 12.01 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1487 helix: 0.67 (0.18), residues: 757 sheet: -1.00 (0.31), residues: 225 loop : -0.36 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 316 HIS 0.017 0.001 HIS A 335 PHE 0.017 0.002 PHE A 98 TYR 0.018 0.001 TYR A1891 ARG 0.005 0.000 ARG A1892 *********************** 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 137 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 1.869 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 outliers start: 12 outliers final: 9 residues processed: 130 average time/residue: 0.7419 time to fit residues: 135.9524 Evaluate side-chains 124 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 2.449 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.4321 time to fit residues: 9.8242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 128 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.8129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 13560 Z= 0.292 Angle : 0.662 8.199 18621 Z= 0.353 Chirality : 0.043 0.796 2169 Planarity : 0.005 0.068 2167 Dihedral : 15.046 161.185 2452 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 23.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.80 % Allowed : 13.96 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.21), residues: 1487 helix: 0.66 (0.19), residues: 744 sheet: -0.98 (0.34), residues: 201 loop : -0.60 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1048 HIS 0.009 0.002 HIS A 83 PHE 0.032 0.003 PHE A 537 TYR 0.034 0.002 TYR A1566 ARG 0.004 0.001 ARG C 353 *********************** 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 143 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 2.115 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 outliers start: 24 outliers final: 18 residues processed: 130 average time/residue: 0.6891 time to fit residues: 127.2866 Evaluate side-chains 129 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.966 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.3717 time to fit residues: 13.6701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.9990 chunk 135 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN ** A1576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.8801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13560 Z= 0.227 Angle : 0.594 7.626 18621 Z= 0.316 Chirality : 0.042 0.788 2169 Planarity : 0.005 0.070 2167 Dihedral : 15.115 160.226 2452 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.83 % Allowed : 15.32 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1487 helix: 0.70 (0.18), residues: 752 sheet: -0.84 (0.34), residues: 209 loop : -0.51 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1048 HIS 0.008 0.001 HIS A1325 PHE 0.013 0.002 PHE A 508 TYR 0.019 0.002 TYR A1566 ARG 0.004 0.000 ARG A1670 *********************** 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 125 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 120 average time/residue: 0.6689 time to fit residues: 115.1309 Evaluate side-chains 117 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 1.928 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.3324 time to fit residues: 7.7117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 40.0000 chunk 17 optimal weight: 0.0980 chunk 85 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 94 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** ** A1576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.8826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13560 Z= 0.153 Angle : 0.538 7.383 18621 Z= 0.278 Chirality : 0.042 0.780 2169 Planarity : 0.004 0.074 2167 Dihedral : 14.836 159.262 2452 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.53 % Allowed : 15.69 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1487 helix: 1.38 (0.19), residues: 748 sheet: -0.62 (0.35), residues: 213 loop : -0.18 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 316 HIS 0.005 0.001 HIS A1325 PHE 0.015 0.002 PHE A1739 TYR 0.018 0.001 TYR A1566 ARG 0.003 0.000 ARG A1060 *********************** 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 133 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 1.848 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 outliers start: 7 outliers final: 7 residues processed: 130 average time/residue: 0.6519 time to fit residues: 118.8430 Evaluate side-chains 128 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 1.915 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.3180 time to fit residues: 6.4237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 144 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.9758 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= 0.237 Angle : 0.602 10.576 18621 Z= 0.321 Chirality : 0.042 0.804 2169 Planarity : 0.005 0.070 2167 Dihedral : 15.030 156.627 2452 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.90 % Allowed : 16.74 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.22), residues: 1487 helix: 1.05 (0.19), residues: 752 sheet: -0.66 (0.35), residues: 215 loop : -0.41 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A1825 HIS 0.011 0.002 HIS A1325 PHE 0.014 0.002 PHE A 572 TYR 0.022 0.002 TYR A 771 ARG 0.005 0.000 ARG A1670 *********************** 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 132 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 1.984 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 outliers start: 12 outliers final: 10 residues processed: 125 average time/residue: 0.6406 time to fit residues: 113.2557 Evaluate side-chains 122 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 2.054 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 10 average time/residue: 0.3068 time to fit residues: 8.1302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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** A1299 GLN ** A1576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 1.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13560 Z= 0.238 Angle : 0.607 8.203 18621 Z= 0.321 Chirality : 0.042 0.808 2169 Planarity : 0.005 0.069 2167 Dihedral : 15.289 155.404 2452 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.90 % Allowed : 16.89 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.22), residues: 1487 helix: 0.93 (0.19), residues: 752 sheet: -0.75 (0.35), residues: 217 loop : -0.51 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 316 HIS 0.010 0.002 HIS A1325 PHE 0.019 0.002 PHE A1700 TYR 0.019 0.002 TYR A1566 ARG 0.009 0.001 ARG A 327 *********************** 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 123 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 2.098 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 outliers start: 12 outliers final: 11 residues processed: 115 average time/residue: 0.6301 time to fit residues: 105.1027 Evaluate side-chains 118 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 1.983 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.3600 time to fit residues: 9.4004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 155 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 75 optimal weight: 0.3980 chunk 98 optimal weight: 6.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN ** A1655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 1.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13560 Z= 0.272 Angle : 0.653 9.908 18621 Z= 0.348 Chirality : 0.043 0.816 2169 Planarity : 0.005 0.067 2167 Dihedral : 15.441 152.110 2452 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 25.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.65 % Favored : 94.28 % Rotamer: Outliers : 0.53 % Allowed : 17.19 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.22), residues: 1487 helix: 0.68 (0.19), residues: 751 sheet: -0.62 (0.36), residues: 208 loop : -0.69 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A1825 HIS 0.014 0.002 HIS A1325 PHE 0.017 0.002 PHE A 508 TYR 0.031 0.002 TYR A 771 ARG 0.021 0.001 ARG A 353 ********************** 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 111 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 1.983 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 outliers start: 7 outliers final: 5 residues processed: 107 average time/residue: 0.6486 time to fit residues: 100.2554 Evaluate side-chains 104 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 1.886 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.3235 time to fit residues: 5.4419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 127 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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** ** A1655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1683 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.079175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.059582 restraints weight = 447623.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.060296 restraints weight = 277675.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.061080 restraints weight = 194523.281| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 1.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13560 Z= 0.188 Angle : 0.570 7.856 18621 Z= 0.299 Chirality : 0.042 0.806 2169 Planarity : 0.005 0.067 2167 Dihedral : 15.313 151.002 2452 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.38 % Allowed : 17.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.22), residues: 1487 helix: 1.03 (0.19), residues: 752 sheet: -0.63 (0.36), residues: 210 loop : -0.57 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 316 HIS 0.009 0.001 HIS A1325 PHE 0.016 0.002 PHE A1806 TYR 0.016 0.001 TYR A 771 ARG 0.011 0.000 ARG A 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5463.98 seconds wall clock time: 98 minutes 25.31 seconds (5905.31 seconds total)