Starting phenix.real_space_refine on Wed Mar 20 01:05:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpk_14856/03_2024/7zpk_14856.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpk_14856/03_2024/7zpk_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_14856/03_2024/7zpk_14856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpk_14856/03_2024/7zpk_14856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpk_14856/03_2024/7zpk_14856.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpk_14856/03_2024/7zpk_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 11.82, per 1000 atoms: 0.46 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: 21.33 Conformation dependent library (CDL) restraints added in 2.2 seconds 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2888 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 12 sheets defined 53.5% alpha, 13.9% beta 18 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 11.96 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: 10.74 Time building geometry restraints manager: 22.17 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: 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 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 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: 0.360 Extract box with map and model: 12.660 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 92.510 Find NCS groups from input model: 0.440 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.620 ------------------------------------------------------------------------------- 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 : 15.299 152.539 5496 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.68 % Allowed : 3.08 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1487 helix: 0.55 (0.17), residues: 738 sheet: -0.44 (0.35), residues: 201 loop : -0.32 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.007 TRP A 316 HIS 0.015 0.003 HIS A1749 PHE 0.033 0.004 PHE C 306 TYR 0.046 0.007 TYR A1695 ARG 0.051 0.006 ARG A 459 *********************** 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 : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 VAL cc_start: 0.8393 (t) cc_final: 0.8190 (t) REVERT: A 230 LEU cc_start: 0.8242 (mm) cc_final: 0.7934 (mm) REVERT: A 381 LEU cc_start: 0.9665 (mt) cc_final: 0.9372 (tp) REVERT: A 637 TYR cc_start: 0.8382 (t80) cc_final: 0.8179 (t80) REVERT: A 1674 LYS cc_start: 0.7797 (mmtt) cc_final: 0.6481 (mmtt) REVERT: A 1683 HIS cc_start: 0.7726 (t-90) cc_final: 0.7396 (t70) REVERT: A 1764 ASP cc_start: 0.7695 (m-30) cc_final: 0.7436 (m-30) outliers start: 9 outliers final: 3 residues processed: 231 average time/residue: 0.6719 time to fit residues: 214.5157 Evaluate side-chains 162 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 159 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 364 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 0.0570 chunk 122 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 overall best weight: 2.5902 ------------------------------------------------------------------------------- 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 ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13560 Z= 0.243 Angle : 0.631 9.010 18621 Z= 0.329 Chirality : 0.042 0.782 2169 Planarity : 0.005 0.072 2167 Dihedral : 15.372 157.555 2520 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.65 % Allowed : 7.21 % Favored : 91.14 % 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: 0.75 (0.21), residues: 1487 helix: 1.22 (0.18), residues: 746 sheet: -0.34 (0.35), residues: 205 loop : -0.01 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 138 HIS 0.008 0.001 HIS A 335 PHE 0.014 0.002 PHE A 894 TYR 0.019 0.002 TYR A1566 ARG 0.015 0.001 ARG A 307 *********************** 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 179 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 157 time to evaluate : 2.004 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: symmetry clash REVERT: A 153 TYR cc_start: 0.9691 (m-10) cc_final: 0.9432 (m-10) REVERT: A 272 MET cc_start: 0.9364 (mtp) cc_final: 0.9159 (mmp) REVERT: A 306 CYS cc_start: 0.9330 (t) cc_final: 0.9090 (p) REVERT: A 381 LEU cc_start: 0.9643 (mt) cc_final: 0.9433 (tp) REVERT: A 562 MET cc_start: 0.5117 (tpp) cc_final: 0.4872 (tpp) REVERT: A 813 ILE cc_start: 0.7414 (pt) cc_final: 0.7115 (mt) REVERT: A 1544 LEU cc_start: 0.8064 (mm) cc_final: 0.7839 (pt) REVERT: A 1683 HIS cc_start: 0.8020 (t-90) cc_final: 0.7660 (t70) REVERT: A 1764 ASP cc_start: 0.8028 (m-30) cc_final: 0.7732 (m-30) outliers start: 22 outliers final: 19 residues processed: 169 average time/residue: 0.6818 time to fit residues: 158.9060 Evaluate side-chains 156 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 324 MET 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 565 ASP Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 886 ASP Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 1062 HIS Chi-restraints excluded: chain A residue 1566 TYR Chi-restraints excluded: chain A residue 1572 GLU Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1713 HIS Chi-restraints excluded: chain A residue 1731 SER Chi-restraints excluded: chain A residue 1760 PHE Chi-restraints excluded: chain A residue 1821 LEU Chi-restraints excluded: chain C residue 180 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 153 optimal weight: 20.0000 chunk 126 optimal weight: 2.9990 chunk 140 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.6054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 13560 Z= 0.392 Angle : 0.816 11.164 18621 Z= 0.442 Chirality : 0.047 0.792 2169 Planarity : 0.007 0.094 2167 Dihedral : 16.117 163.244 2519 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 31.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.51 % Favored : 95.29 % Rotamer: Outliers : 2.93 % Allowed : 8.93 % Favored : 88.14 % 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: -0.54 (0.21), residues: 1487 helix: 0.20 (0.18), residues: 749 sheet: -0.90 (0.33), residues: 207 loop : -0.73 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1825 HIS 0.046 0.003 HIS A1062 PHE 0.028 0.003 PHE A 98 TYR 0.034 0.003 TYR A1748 ARG 0.014 0.001 ARG A 459 *********************** 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 180 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 141 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 TYR cc_start: 0.9767 (m-10) cc_final: 0.9561 (m-10) REVERT: A 190 MET cc_start: 0.6877 (ttt) cc_final: 0.6672 (ttt) REVERT: A 306 CYS cc_start: 0.9457 (OUTLIER) cc_final: 0.9233 (p) REVERT: A 471 LEU cc_start: 0.8343 (mt) cc_final: 0.8128 (mt) REVERT: A 1060 ARG cc_start: 0.8975 (tpp80) cc_final: 0.8766 (tpp80) REVERT: A 1560 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6527 (mt-10) REVERT: A 1671 PHE cc_start: 0.8614 (m-10) cc_final: 0.8273 (m-10) REVERT: A 1755 VAL cc_start: 0.9213 (t) cc_final: 0.8947 (t) outliers start: 39 outliers final: 32 residues processed: 168 average time/residue: 0.6225 time to fit residues: 146.3271 Evaluate side-chains 155 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 122 time to evaluate : 2.032 ------------------------------------------------------------------------------- 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 211 ASN Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 324 MET 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 565 ASP Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 637 TYR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 771 TYR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 850 HIS Chi-restraints excluded: chain A residue 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 1062 HIS Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1566 TYR Chi-restraints excluded: chain A residue 1572 GLU Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1709 LEU Chi-restraints excluded: chain A residue 1731 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 364 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 30.0000 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 150 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.7023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13560 Z= 0.247 Angle : 0.619 7.454 18621 Z= 0.331 Chirality : 0.043 0.777 2169 Planarity : 0.005 0.063 2167 Dihedral : 15.932 162.524 2519 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.33 % Allowed : 11.64 % Favored : 86.04 % 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: 0.02 (0.21), residues: 1487 helix: 0.72 (0.18), residues: 746 sheet: -0.91 (0.32), residues: 214 loop : -0.42 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 316 HIS 0.011 0.002 HIS A 335 PHE 0.020 0.002 PHE A1739 TYR 0.018 0.002 TYR A1566 ARG 0.008 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 156 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 2.061 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 153 TYR cc_start: 0.9782 (m-10) cc_final: 0.9574 (m-10) REVERT: A 562 MET cc_start: 0.7016 (tpp) cc_final: 0.6790 (tpp) REVERT: A 565 ASP cc_start: 0.9589 (OUTLIER) cc_final: 0.9128 (t0) REVERT: A 842 MET cc_start: 0.9044 (mmt) cc_final: 0.8828 (mmt) REVERT: A 844 GLU cc_start: 0.9328 (OUTLIER) cc_final: 0.9098 (mm-30) REVERT: A 897 MET cc_start: 0.8841 (ttm) cc_final: 0.8427 (ttp) REVERT: A 1560 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6696 (mt-10) REVERT: A 1671 PHE cc_start: 0.8633 (m-10) cc_final: 0.8184 (m-10) outliers start: 31 outliers final: 25 residues processed: 148 average time/residue: 0.6376 time to fit residues: 132.7818 Evaluate side-chains 140 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 1.706 ------------------------------------------------------------------------------- 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 317 CYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 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 779 THR Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 895 LYS Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1066 THR 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 1656 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1709 LEU Chi-restraints excluded: chain A residue 1731 SER Chi-restraints excluded: chain A residue 1832 MET Chi-restraints excluded: chain C residue 342 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 chunk 135 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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** ** A1749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.8155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13560 Z= 0.243 Angle : 0.624 7.803 18621 Z= 0.327 Chirality : 0.043 0.795 2169 Planarity : 0.005 0.066 2167 Dihedral : 15.843 160.838 2519 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.08 % Allowed : 12.46 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.22), residues: 1487 helix: 0.96 (0.19), residues: 748 sheet: -0.94 (0.33), residues: 213 loop : -0.40 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A1380 HIS 0.011 0.002 HIS A1325 PHE 0.016 0.002 PHE A 174 TYR 0.023 0.002 TYR A 771 ARG 0.007 0.001 ARG A 459 *********************** 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 164 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 123 time to evaluate : 2.004 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 844 GLU cc_start: 0.9402 (OUTLIER) cc_final: 0.9156 (mm-30) REVERT: A 1375 ASP cc_start: 0.9640 (t0) cc_final: 0.9402 (p0) REVERT: A 1560 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6870 (mt-10) REVERT: A 1671 PHE cc_start: 0.8670 (m-10) cc_final: 0.8235 (m-10) outliers start: 41 outliers final: 32 residues processed: 149 average time/residue: 0.6558 time to fit residues: 138.0363 Evaluate side-chains 150 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 117 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 565 ASP 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 771 TYR Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 850 HIS Chi-restraints excluded: chain A residue 886 ASP 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 1066 THR Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1566 TYR Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1687 HIS Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain A residue 1709 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.6980 chunk 135 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 150 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.9391 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= 0.261 Angle : 0.630 9.434 18621 Z= 0.335 Chirality : 0.042 0.792 2169 Planarity : 0.005 0.072 2167 Dihedral : 16.132 157.972 2519 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.60 % Allowed : 13.36 % Favored : 83.03 % 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: -0.11 (0.21), residues: 1487 helix: 0.60 (0.18), residues: 751 sheet: -1.10 (0.33), residues: 207 loop : -0.41 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 316 HIS 0.010 0.002 HIS A1062 PHE 0.017 0.002 PHE A 537 TYR 0.021 0.002 TYR A1829 ARG 0.008 0.000 ARG A 459 *********************** 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 166 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 118 time to evaluate : 2.171 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: A 562 MET cc_start: 0.7275 (tpp) cc_final: 0.7069 (tpp) REVERT: A 672 ASN cc_start: 0.8850 (t0) cc_final: 0.8267 (p0) REVERT: A 844 GLU cc_start: 0.9391 (OUTLIER) cc_final: 0.9144 (mm-30) REVERT: A 992 HIS cc_start: 0.7591 (m170) cc_final: 0.7216 (t-90) REVERT: A 1560 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6882 (mt-10) REVERT: A 1566 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.7432 (m-80) outliers start: 48 outliers final: 44 residues processed: 152 average time/residue: 0.6208 time to fit residues: 134.1371 Evaluate side-chains 160 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 114 time to evaluate : 1.769 ------------------------------------------------------------------------------- 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 211 ASN Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 324 MET 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 538 ASP Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 586 LEU 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 779 THR 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 886 ASP Chi-restraints excluded: chain A residue 895 LYS 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 1066 THR 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 1566 TYR Chi-restraints excluded: chain A residue 1651 LYS 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 1687 HIS 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 1832 MET Chi-restraints excluded: chain A residue 1835 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 342 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 84 optimal weight: 0.2980 chunk 150 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.9459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13560 Z= 0.159 Angle : 0.546 9.803 18621 Z= 0.283 Chirality : 0.041 0.787 2169 Planarity : 0.005 0.070 2167 Dihedral : 15.877 156.904 2517 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.63 % Allowed : 14.64 % Favored : 82.73 % 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: 0.53 (0.22), residues: 1487 helix: 1.25 (0.19), residues: 749 sheet: -0.94 (0.33), residues: 219 loop : -0.23 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 316 HIS 0.006 0.001 HIS A 850 PHE 0.016 0.002 PHE A1739 TYR 0.015 0.001 TYR A 771 ARG 0.005 0.000 ARG A 459 *********************** 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 154 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 119 time to evaluate : 1.909 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 897 MET cc_start: 0.9102 (ttm) cc_final: 0.8745 (ttp) REVERT: A 992 HIS cc_start: 0.7481 (m170) cc_final: 0.7121 (t-90) REVERT: A 1375 ASP cc_start: 0.9668 (t0) cc_final: 0.9421 (p0) REVERT: A 1557 ASP cc_start: 0.8113 (m-30) cc_final: 0.7838 (m-30) REVERT: A 1579 LEU cc_start: 0.9447 (mm) cc_final: 0.9233 (mt) outliers start: 35 outliers final: 33 residues processed: 145 average time/residue: 0.6263 time to fit residues: 128.4808 Evaluate side-chains 147 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 114 time to evaluate : 1.973 ------------------------------------------------------------------------------- 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 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 779 THR Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 895 LYS Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 995 SER Chi-restraints excluded: chain A residue 1004 HIS Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1545 HIS Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1651 LYS 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 1687 HIS 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 1821 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 1.0099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13560 Z= 0.205 Angle : 0.567 9.501 18621 Z= 0.299 Chirality : 0.041 0.798 2169 Planarity : 0.005 0.075 2167 Dihedral : 15.904 154.182 2517 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.08 % Allowed : 14.79 % 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: 0.51 (0.22), residues: 1487 helix: 1.20 (0.19), residues: 750 sheet: -0.85 (0.34), residues: 218 loop : -0.23 (0.29), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 316 HIS 0.008 0.001 HIS A1062 PHE 0.015 0.002 PHE A 894 TYR 0.033 0.002 TYR A1566 ARG 0.008 0.000 ARG A 353 *********************** 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 156 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 115 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 672 ASN cc_start: 0.8947 (t0) cc_final: 0.8448 (p0) REVERT: A 844 GLU cc_start: 0.9477 (OUTLIER) cc_final: 0.9235 (mm-30) REVERT: A 992 HIS cc_start: 0.7929 (m170) cc_final: 0.7645 (t-90) outliers start: 41 outliers final: 37 residues processed: 141 average time/residue: 0.6177 time to fit residues: 122.8144 Evaluate side-chains 148 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 110 time to evaluate : 1.801 ------------------------------------------------------------------------------- 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 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 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 775 MET Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 850 HIS Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 995 SER 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 1066 THR Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1651 LYS Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1687 HIS 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 1809 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 9.9990 chunk 140 optimal weight: 50.0000 chunk 144 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 850 HIS A1299 GLN ** A1655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 1.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 13560 Z= 0.294 Angle : 0.658 11.155 18621 Z= 0.352 Chirality : 0.043 0.817 2169 Planarity : 0.006 0.072 2167 Dihedral : 16.353 152.929 2517 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 25.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.38 % Allowed : 15.02 % Favored : 81.61 % 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: -0.02 (0.22), residues: 1487 helix: 0.72 (0.18), residues: 747 sheet: -1.17 (0.33), residues: 223 loop : -0.36 (0.29), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1825 HIS 0.010 0.002 HIS A 83 PHE 0.016 0.002 PHE A1322 TYR 0.029 0.002 TYR A1566 ARG 0.008 0.001 ARG A 459 *********************** 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 153 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 108 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 MET cc_start: 0.7187 (tpp) cc_final: 0.6724 (mmm) REVERT: A 672 ASN cc_start: 0.9206 (t0) cc_final: 0.8752 (p0) REVERT: A 842 MET cc_start: 0.9434 (tpp) cc_final: 0.9208 (tpp) REVERT: A 844 GLU cc_start: 0.9511 (OUTLIER) cc_final: 0.9291 (mm-30) REVERT: A 1316 GLU cc_start: 0.8766 (tt0) cc_final: 0.8535 (tt0) REVERT: A 1813 ILE cc_start: 0.8666 (mm) cc_final: 0.8309 (mm) outliers start: 45 outliers final: 44 residues processed: 142 average time/residue: 0.6293 time to fit residues: 126.0651 Evaluate side-chains 149 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 104 time to evaluate : 1.661 ------------------------------------------------------------------------------- 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 317 CYS Chi-restraints excluded: chain A residue 324 MET 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 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 775 MET Chi-restraints excluded: chain A residue 779 THR 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 995 SER 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 1066 THR 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 1584 LEU Chi-restraints excluded: chain A residue 1651 LYS Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1670 ARG Chi-restraints excluded: chain A residue 1687 HIS 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 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 148 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 143 optimal weight: 20.0000 chunk 123 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 98 optimal weight: 0.4980 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 ** A1655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 1.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13560 Z= 0.190 Angle : 0.577 8.847 18621 Z= 0.302 Chirality : 0.042 0.805 2169 Planarity : 0.005 0.071 2167 Dihedral : 16.186 151.905 2517 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.78 % Allowed : 16.07 % Favored : 81.16 % 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: 0.29 (0.22), residues: 1487 helix: 1.05 (0.19), residues: 750 sheet: -0.94 (0.35), residues: 207 loop : -0.41 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 316 HIS 0.015 0.001 HIS A 850 PHE 0.015 0.002 PHE A1806 TYR 0.019 0.001 TYR A1566 ARG 0.007 0.000 ARG A1670 ********************** 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 143 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 106 time to evaluate : 2.040 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 672 ASN cc_start: 0.9185 (t0) cc_final: 0.8758 (p0) REVERT: A 842 MET cc_start: 0.9446 (tpp) cc_final: 0.9140 (tpp) REVERT: A 897 MET cc_start: 0.9228 (ttm) cc_final: 0.8800 (ttp) REVERT: A 1813 ILE cc_start: 0.8600 (mm) cc_final: 0.8226 (mm) outliers start: 37 outliers final: 35 residues processed: 134 average time/residue: 0.6422 time to fit residues: 121.8339 Evaluate side-chains 138 residues out of total 1337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 103 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 150 MET 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 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 708 LEU Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain A residue 779 THR 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 979 ASP Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 995 SER Chi-restraints excluded: chain A residue 1004 HIS Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1651 LYS 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 1687 HIS Chi-restraints excluded: chain A residue 1693 ASP Chi-restraints excluded: chain A residue 1709 LEU 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 131 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 chunk 15 optimal weight: 0.0770 chunk 22 optimal weight: 8.9990 chunk 108 optimal weight: 0.3980 overall best weight: 2.6942 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.076561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.058077 restraints weight = 449181.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.058178 restraints weight = 281427.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.058966 restraints weight = 197574.581| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 1.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13560 Z= 0.216 Angle : 0.598 10.866 18621 Z= 0.312 Chirality : 0.042 0.810 2169 Planarity : 0.005 0.066 2167 Dihedral : 16.124 148.429 2517 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.48 % Allowed : 16.59 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.37 (0.22), residues: 1487 helix: 1.16 (0.19), residues: 750 sheet: -0.90 (0.35), residues: 207 loop : -0.47 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 316 HIS 0.008 0.002 HIS A1545 PHE 0.015 0.002 PHE A 572 TYR 0.022 0.002 TYR A1566 ARG 0.009 0.001 ARG A1670 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5530.48 seconds wall clock time: 98 minutes 52.26 seconds (5932.26 seconds total)