Starting phenix.real_space_refine (version: dev) on Fri Feb 24 16:17:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpj_14855/02_2023/7zpj_14855.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpj_14855/02_2023/7zpj_14855.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/7zpj_14855/02_2023/7zpj_14855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpj_14855/02_2023/7zpj_14855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpj_14855/02_2023/7zpj_14855.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpj_14855/02_2023/7zpj_14855.pdb" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.019 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 23479 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 20612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1280, 20612 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: "D" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1104 Classifications: {'peptide': 75} Link IDs: {'PCIS': 1, 'TRANS': 73} Time building chain proxies: 11.38, per 1000 atoms: 0.48 Number of scatterers: 23479 At special positions: 0 Unit cell: (98.53, 122.745, 163.66, 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 63 16.00 P 55 15.00 O 2382 8.00 N 2043 7.00 C 7428 6.00 H 11508 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: 19.71 Conformation dependent library (CDL) restraints added in 1.8 seconds 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 10 sheets defined 53.6% alpha, 12.4% beta 17 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 9.48 Creating SS restraints... Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.527A pdb=" N LYS A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) 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 102 through 117 Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 4.147A 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 177 through 181 Processing helix chain 'A' and resid 184 through 196 removed outlier: 4.292A pdb=" N GLU A 188 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 231 removed outlier: 5.037A 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: 3.855A 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: 3.653A 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: 3.661A 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 520 through 524 Processing helix chain 'A' and resid 542 through 551 Processing helix chain 'A' and resid 565 through 592 removed outlier: 3.981A pdb=" N LYS A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER A 571 " --> pdb=" O ASP A 567 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU A 574 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 641 removed outlier: 4.317A pdb=" N GLY A 632 " --> pdb=" O ASN A 628 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 641 " --> pdb=" O TYR A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 706 removed outlier: 3.565A 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: 4.085A 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 1351 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: 3.659A pdb=" N GLY A1571 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLU A1572 " --> pdb=" O THR A1568 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N ARG A1573 " --> pdb=" O SER A1569 " (cutoff:3.500A) removed outlier: 4.188A 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: 3.728A pdb=" N LYS A1666 " --> pdb=" O THR A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1674 through 1682 removed outlier: 3.787A pdb=" N LEU A1678 " --> pdb=" O LYS A1674 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1716 removed outlier: 3.616A pdb=" N PHE A1700 " --> pdb=" O GLN A1696 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A1701 " --> pdb=" O ARG A1697 " (cutoff:3.500A) removed outlier: 3.573A 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: 4.020A pdb=" N TYR A1751 " --> pdb=" O ASP A1747 " (cutoff:3.500A) Processing helix chain 'A' and resid 1756 through 1773 removed outlier: 3.590A pdb=" N LYS A1768 " --> pdb=" O ASP A1764 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS A1773 " --> pdb=" O PHE A1769 " (cutoff:3.500A) Processing helix chain 'A' and resid 1799 through 1817 removed outlier: 3.868A pdb=" N GLY A1803 " --> pdb=" O PRO A1799 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1842 removed outlier: 3.509A pdb=" N VAL A1824 " --> pdb=" O SER A1820 " (cutoff:3.500A) Proline residue: A1830 - end of helix Proline residue: A1834 - end of helix removed outlier: 3.933A 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 'D' and resid 292 through 304 Processing helix chain 'D' and resid 342 through 364 Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.942A pdb=" N THR A 151 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR A 96 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N MET A 150 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N PHE A 98 " --> pdb=" O MET A 150 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ARG A 95 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU A 171 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 97 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 173 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP A 175 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR A 60 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N THR A 206 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL A 62 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 5.977A 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: 6.166A pdb=" N CYS A 251 " --> pdb=" O TYR A 560 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET A 562 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 253 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ALA A 564 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL A 255 " --> pdb=" O ALA A 564 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A 445 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.616A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 816 through 820 removed outlier: 3.800A pdb=" N PHE A 816 " --> pdb=" O ILE A 827 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N GLU A 824 " --> pdb=" O THR A 778 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A 832 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU A 770 " --> pdb=" O LYS A 832 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N SER A 834 " --> pdb=" O CYS A 768 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N CYS A 768 " --> pdb=" O SER A 834 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N PHE A 802 " --> pdb=" O ILE A 773 " (cutoff:3.500A) removed outlier: 4.742A 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: 6.176A pdb=" N ASP A 991 " --> pdb=" O VAL A 947 " (cutoff:3.500A) removed outlier: 5.718A 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 'D' and resid 308 through 312 581 hydrogen bonds defined for protein. 1671 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 10.05 Time building geometry restraints manager: 20.20 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: 11467 1.02 - 1.22: 49 1.22 - 1.42: 5060 1.42 - 1.62: 7181 1.62 - 1.82: 85 Bond restraints: 23842 Sorted by residual: bond pdb=" NH1 ARG A 86 " pdb="HH12 ARG A 86 " ideal model delta sigma weight residual 0.860 0.819 0.041 2.00e-02 2.50e+03 4.11e+00 bond pdb=" NH1 ARG A 800 " pdb="HH12 ARG A 800 " ideal model delta sigma weight residual 0.860 0.826 0.034 2.00e-02 2.50e+03 2.89e+00 bond pdb=" NE2 GLN A 985 " pdb="HE22 GLN A 985 " ideal model delta sigma weight residual 0.860 0.828 0.032 2.00e-02 2.50e+03 2.59e+00 bond pdb=" C ILE A 773 " pdb=" N GLY A 774 " ideal model delta sigma weight residual 1.330 1.319 0.011 8.80e-03 1.29e+04 1.67e+00 bond pdb=" NH2 ARG A 640 " pdb="HH22 ARG A 640 " ideal model delta sigma weight residual 0.860 0.835 0.025 2.00e-02 2.50e+03 1.62e+00 ... (remaining 23837 not shown) Histogram of bond angle deviations from ideal: 71.09 - 83.68: 6 83.68 - 96.27: 1 96.27 - 108.86: 10432 108.86 - 121.46: 28288 121.46 - 134.05: 4450 Bond angle restraints: 43177 Sorted by residual: angle pdb=" CB ALA A 464 " pdb=" CA ALA A 464 " pdb=" HA ALA A 464 " ideal model delta sigma weight residual 109.00 71.09 37.91 3.00e+00 1.11e-01 1.60e+02 angle pdb=" N ALA A 464 " pdb=" CA ALA A 464 " pdb=" HA ALA A 464 " ideal model delta sigma weight residual 110.00 75.34 34.66 3.00e+00 1.11e-01 1.34e+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 76.55 32.45 3.00e+00 1.11e-01 1.17e+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 77.57 31.43 3.00e+00 1.11e-01 1.10e+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 79.64 29.36 3.00e+00 1.11e-01 9.58e+01 ... (remaining 43172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 9429 35.91 - 71.81: 154 71.81 - 107.72: 14 107.72 - 143.63: 1 143.63 - 179.53: 9 Dihedral angle restraints: 9607 sinusoidal: 4953 harmonic: 4654 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 55.37 144.63 1 1.50e+01 4.44e-03 7.75e+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 60.31 139.69 1 1.50e+01 4.44e-03 7.52e+01 dihedral pdb=" CG TRP A 316 " pdb=" CD2 TRP A 316 " pdb=" CE3 TRP A 316 " pdb=" HE3 TRP A 316 " ideal model delta harmonic sigma weight residual 0.00 24.94 -24.94 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 9604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 1970 0.183 - 0.365: 12 0.365 - 0.548: 0 0.548 - 0.730: 0 0.730 - 0.913: 1 Chirality restraints: 1983 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 -1.56 -0.91 2.00e-01 2.50e+01 2.08e+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 2.18 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" P U B 28 " pdb=" OP1 U B 28 " pdb=" OP2 U B 28 " pdb=" O5' U B 28 " both_signs ideal model delta sigma weight residual True 2.41 -2.71 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 1980 not shown) Planarity restraints: 3263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 316 " 0.028 2.00e-02 2.50e+03 6.16e-02 1.52e+02 pdb=" CG TRP A 316 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 316 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 316 " -0.023 2.00e-02 2.50e+03 pdb=" NE1 TRP A 316 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TRP A 316 " -0.040 2.00e-02 2.50e+03 pdb=" CE3 TRP A 316 " 0.120 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 316 " -0.061 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 316 " -0.105 2.00e-02 2.50e+03 pdb=" CH2 TRP A 316 " -0.077 2.00e-02 2.50e+03 pdb=" HD1 TRP A 316 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 TRP A 316 " 0.046 2.00e-02 2.50e+03 pdb=" HE3 TRP A 316 " -0.057 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 316 " 0.063 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 316 " 0.054 2.00e-02 2.50e+03 pdb=" HH2 TRP A 316 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 86 " -0.268 9.50e-02 1.11e+02 1.16e-01 1.30e+02 pdb=" NE ARG A 86 " -0.081 2.00e-02 2.50e+03 pdb=" CZ ARG A 86 " 0.082 2.00e-02 2.50e+03 pdb=" NH1 ARG A 86 " 0.126 2.00e-02 2.50e+03 pdb=" NH2 ARG A 86 " 0.043 2.00e-02 2.50e+03 pdb="HH11 ARG A 86 " 0.011 2.00e-02 2.50e+03 pdb="HH12 ARG A 86 " -0.125 2.00e-02 2.50e+03 pdb="HH21 ARG A 86 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 86 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 187 " -0.421 9.50e-02 1.11e+02 1.51e-01 9.05e+01 pdb=" NE ARG A 187 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG A 187 " 0.053 2.00e-02 2.50e+03 pdb=" NH1 ARG A 187 " 0.077 2.00e-02 2.50e+03 pdb=" NH2 ARG A 187 " 0.080 2.00e-02 2.50e+03 pdb="HH11 ARG A 187 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 187 " -0.062 2.00e-02 2.50e+03 pdb="HH21 ARG A 187 " 0.003 2.00e-02 2.50e+03 pdb="HH22 ARG A 187 " -0.082 2.00e-02 2.50e+03 ... (remaining 3260 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1023 2.18 - 2.78: 46703 2.78 - 3.39: 65218 3.39 - 3.99: 81336 3.99 - 4.60: 127023 Nonbonded interactions: 321303 Sorted by model distance: nonbonded pdb="HH21 ARG A 935 " pdb=" O GLU A1036 " model vdw 1.574 1.850 nonbonded pdb=" HG1 THR A1867 " pdb=" OD1 ASP A1869 " model vdw 1.582 1.850 nonbonded pdb=" O LEU A1678 " pdb=" HG1 THR A1682 " model vdw 1.594 1.850 nonbonded pdb=" O GLU A 542 " pdb=" HG SER A 545 " model vdw 1.603 1.850 nonbonded pdb=" OE1 GLU A 866 " pdb=" HZ2 LYS A 868 " model vdw 1.605 1.850 ... (remaining 321298 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 55 5.49 5 S 63 5.16 5 C 7428 2.51 5 N 2043 2.21 5 O 2382 1.98 5 H 11508 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.310 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: 0.330 Extract box with map and model: 13.270 Check model and map are aligned: 0.370 Process input model: 85.120 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.230 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3304 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 0.047 12334 Z= 0.288 Angle : 0.864 10.310 16970 Z= 0.501 Chirality : 0.054 0.913 1983 Planarity : 0.015 0.245 1955 Dihedral : 13.186 144.630 4817 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 1333 helix: 0.77 (0.18), residues: 672 sheet: -0.58 (0.37), residues: 180 loop : -0.28 (0.29), residues: 481 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 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 216 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 208 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 215 average time/residue: 0.6448 time to fit residues: 190.1462 Evaluate side-chains 171 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 166 time to evaluate : 1.750 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.2753 time to fit residues: 4.8282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 109 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A1548 GLN ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3930 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 12334 Z= 0.266 Angle : 0.653 7.593 16970 Z= 0.348 Chirality : 0.044 0.773 1983 Planarity : 0.005 0.105 1955 Dihedral : 10.447 154.502 2139 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.42 (0.22), residues: 1333 helix: 1.04 (0.19), residues: 673 sheet: -0.66 (0.37), residues: 189 loop : -0.26 (0.29), residues: 471 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 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 192 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 181 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 188 average time/residue: 0.6591 time to fit residues: 169.9143 Evaluate side-chains 172 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 163 time to evaluate : 1.752 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2712 time to fit residues: 6.8737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN ** A1654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4206 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 12334 Z= 0.212 Angle : 0.583 8.142 16970 Z= 0.308 Chirality : 0.042 0.769 1983 Planarity : 0.005 0.040 1955 Dihedral : 10.185 156.873 2139 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.60 (0.23), residues: 1333 helix: 1.28 (0.20), residues: 678 sheet: -0.97 (0.37), residues: 188 loop : -0.15 (0.29), residues: 467 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 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 182 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 172 time to evaluate : 1.684 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 outliers start: 10 outliers final: 9 residues processed: 176 average time/residue: 0.6197 time to fit residues: 150.7112 Evaluate side-chains 171 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 1.575 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.2885 time to fit residues: 6.6787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 0.0270 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 135 optimal weight: 20.0000 chunk 121 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 112 optimal weight: 0.8980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4308 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 12334 Z= 0.169 Angle : 0.527 7.658 16970 Z= 0.277 Chirality : 0.041 0.772 1983 Planarity : 0.004 0.047 1955 Dihedral : 10.176 159.011 2139 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.77 (0.23), residues: 1333 helix: 1.45 (0.20), residues: 682 sheet: -0.97 (0.36), residues: 197 loop : -0.08 (0.30), residues: 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 171 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 178 average time/residue: 0.6311 time to fit residues: 154.6770 Evaluate side-chains 173 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 166 time to evaluate : 1.816 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.2647 time to fit residues: 5.9305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 841 GLN ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1683 HIS ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4900 moved from start: 0.6868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 12334 Z= 0.302 Angle : 0.686 10.759 16970 Z= 0.368 Chirality : 0.046 0.774 1983 Planarity : 0.006 0.088 1955 Dihedral : 10.522 160.363 2139 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.48 % Favored : 94.45 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -0.14 (0.23), residues: 1333 helix: 0.66 (0.20), residues: 679 sheet: -1.06 (0.37), residues: 178 loop : -0.63 (0.28), residues: 476 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 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 217 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 197 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 15 residues processed: 207 average time/residue: 0.6336 time to fit residues: 180.1273 Evaluate side-chains 195 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 180 time to evaluate : 1.702 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.3121 time to fit residues: 10.2790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 135 optimal weight: 0.0870 chunk 112 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 71 optimal weight: 0.0670 chunk 130 optimal weight: 9.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 938 ASN ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4788 moved from start: 0.7214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.074 12334 Z= 0.153 Angle : 0.533 7.573 16970 Z= 0.279 Chirality : 0.041 0.775 1983 Planarity : 0.004 0.053 1955 Dihedral : 10.320 161.374 2139 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.45 (0.23), residues: 1333 helix: 1.20 (0.20), residues: 684 sheet: -0.80 (0.38), residues: 176 loop : -0.46 (0.29), residues: 473 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 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 189 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 179 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 184 average time/residue: 0.6282 time to fit residues: 159.8439 Evaluate side-chains 180 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 173 time to evaluate : 1.692 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.2834 time to fit residues: 5.7199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 82 optimal weight: 0.2980 chunk 62 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 943 HIS ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5057 moved from start: 0.8192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 12334 Z= 0.212 Angle : 0.567 9.366 16970 Z= 0.302 Chirality : 0.042 0.775 1983 Planarity : 0.005 0.049 1955 Dihedral : 10.358 161.533 2139 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.40 (0.23), residues: 1333 helix: 1.21 (0.20), residues: 683 sheet: -0.85 (0.36), residues: 202 loop : -0.52 (0.30), residues: 448 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 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 199 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 187 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 192 average time/residue: 0.6286 time to fit residues: 167.5428 Evaluate side-chains 189 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 180 time to evaluate : 1.697 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.4020 time to fit residues: 7.7905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1355 ASN ** A1655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1770 GLN ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5622 moved from start: 1.0617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 12334 Z= 0.353 Angle : 0.799 11.587 16970 Z= 0.434 Chirality : 0.050 0.785 1983 Planarity : 0.008 0.117 1955 Dihedral : 11.215 162.001 2139 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 23.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.23 % Favored : 93.70 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.22), residues: 1333 helix: -0.05 (0.19), residues: 679 sheet: -1.25 (0.35), residues: 195 loop : -1.22 (0.29), residues: 459 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 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 238 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 220 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 227 average time/residue: 0.5996 time to fit residues: 188.8888 Evaluate side-chains 222 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 208 time to evaluate : 1.771 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.3036 time to fit residues: 9.5257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.7980 chunk 125 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 118 optimal weight: 0.2980 chunk 82 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 GLN ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 moved from start: 1.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 12334 Z= 0.194 Angle : 0.612 7.846 16970 Z= 0.323 Chirality : 0.043 0.776 1983 Planarity : 0.006 0.077 1955 Dihedral : 10.820 162.848 2139 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.23), residues: 1333 helix: 0.82 (0.20), residues: 674 sheet: -1.10 (0.35), residues: 198 loop : -1.00 (0.29), residues: 461 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 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 224 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 215 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 218 average time/residue: 0.6383 time to fit residues: 192.1419 Evaluate side-chains 214 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 207 time to evaluate : 1.696 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.3187 time to fit residues: 6.0294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 0.0870 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1770 GLN ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5575 moved from start: 1.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 12334 Z= 0.197 Angle : 0.607 9.463 16970 Z= 0.321 Chirality : 0.043 0.776 1983 Planarity : 0.005 0.054 1955 Dihedral : 10.717 162.886 2139 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -0.10 (0.23), residues: 1333 helix: 0.87 (0.20), residues: 672 sheet: -0.99 (0.36), residues: 203 loop : -0.89 (0.30), residues: 458 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 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 221 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 216 time to evaluate : 1.895 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 outliers start: 5 outliers final: 5 residues processed: 216 average time/residue: 0.6121 time to fit residues: 183.6136 Evaluate side-chains 215 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 210 time to evaluate : 1.724 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.2811 time to fit residues: 4.8592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 0.0170 chunk 46 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS ** A1355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.188259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.150609 restraints weight = 70028.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.158543 restraints weight = 33618.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.163624 restraints weight = 19070.649| |-----------------------------------------------------------------------------| r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5717 moved from start: 1.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 12334 Z= 0.221 Angle : 0.623 12.069 16970 Z= 0.332 Chirality : 0.043 0.776 1983 Planarity : 0.005 0.053 1955 Dihedral : 10.767 162.814 2139 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.23), residues: 1333 helix: 0.82 (0.20), residues: 678 sheet: -0.93 (0.36), residues: 198 loop : -0.92 (0.30), residues: 457 =============================================================================== Job complete usr+sys time: 5679.42 seconds wall clock time: 101 minutes 14.08 seconds (6074.08 seconds total)