Starting phenix.real_space_refine on Tue Mar 19 05:50:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpj_14855/03_2024/7zpj_14855.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpj_14855/03_2024/7zpj_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_14855/03_2024/7zpj_14855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpj_14855/03_2024/7zpj_14855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpj_14855/03_2024/7zpj_14855.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpj_14855/03_2024/7zpj_14855.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= 0.019 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 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. 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-5265/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: 10.40, per 1000 atoms: 0.44 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: 19.68 Conformation dependent library (CDL) restraints added in 2.3 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: 11.20 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: 10.69 Time building geometry restraints manager: 20.63 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: 10952 35.91 - 71.81: 343 71.81 - 107.72: 23 107.72 - 143.63: 1 143.63 - 179.53: 9 Dihedral angle restraints: 11328 sinusoidal: 6674 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 11325 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.920 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: 0.030 Extract box with map and model: 12.460 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 86.430 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.080 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3446 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 : 15.404 144.630 5027 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 % Allowed : 2.49 % Favored : 96.84 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.116 0.010 TRP A 316 HIS 0.016 0.003 HIS A1749 PHE 0.055 0.004 PHE A 537 TYR 0.039 0.007 TYR A1676 ARG 0.066 0.006 ARG A 459 *********************** 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 : 1.615 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: A 269 ARG cc_start: 0.8394 (ttt180) cc_final: 0.7666 (mtm180) REVERT: A 272 MET cc_start: 0.7855 (mtp) cc_final: 0.7156 (mtp) REVERT: A 377 VAL cc_start: 0.8626 (t) cc_final: 0.8384 (m) REVERT: A 379 LYS cc_start: 0.8641 (mmtt) cc_final: 0.8275 (mmtm) REVERT: A 503 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7178 (mt-10) REVERT: A 710 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7582 (tp30) REVERT: A 940 ASP cc_start: 0.2701 (OUTLIER) cc_final: 0.2303 (m-30) REVERT: A 1368 ARG cc_start: 0.4125 (mmt90) cc_final: 0.3905 (mpt-90) REVERT: A 1825 TRP cc_start: 0.2199 (t-100) cc_final: 0.1957 (t60) outliers start: 8 outliers final: 5 residues processed: 215 average time/residue: 0.6299 time to fit residues: 185.2550 Evaluate side-chains 172 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 166 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 940 ASP Chi-restraints excluded: chain D residue 364 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.3977 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12334 Z= 0.239 Angle : 0.625 8.037 16970 Z= 0.331 Chirality : 0.043 0.769 1983 Planarity : 0.005 0.098 1955 Dihedral : 15.895 154.111 2360 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.83 % Allowed : 5.90 % Favored : 93.27 % 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: 0.69 (0.23), residues: 1333 helix: 1.22 (0.19), residues: 674 sheet: -0.43 (0.38), residues: 183 loop : -0.12 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 316 HIS 0.005 0.001 HIS A 116 PHE 0.053 0.002 PHE A 142 TYR 0.021 0.002 TYR A1746 ARG 0.007 0.001 ARG A 640 *********************** 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 189 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 179 time to evaluate : 1.634 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: A 168 ASP cc_start: 0.6445 (m-30) cc_final: 0.5437 (p0) REVERT: A 206 THR cc_start: 0.3155 (t) cc_final: 0.2879 (t) REVERT: A 272 MET cc_start: 0.7963 (mtp) cc_final: 0.7315 (mtp) REVERT: A 307 ARG cc_start: 0.7436 (ttt-90) cc_final: 0.7143 (ttp80) REVERT: A 503 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7293 (mt-10) REVERT: A 831 LEU cc_start: 0.4503 (tt) cc_final: 0.4301 (tt) REVERT: A 1363 LYS cc_start: 0.7254 (mmtt) cc_final: 0.6950 (mptt) REVERT: A 1558 CYS cc_start: 0.1982 (OUTLIER) cc_final: 0.1721 (t) REVERT: A 1825 TRP cc_start: 0.2150 (t-100) cc_final: 0.0455 (t-100) outliers start: 10 outliers final: 8 residues processed: 185 average time/residue: 0.6479 time to fit residues: 163.8779 Evaluate side-chains 175 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 166 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 1548 GLN Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1722 SER Chi-restraints excluded: chain D residue 364 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 HIS ** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN A1548 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4580 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 12334 Z= 0.311 Angle : 0.650 8.409 16970 Z= 0.350 Chirality : 0.045 0.773 1983 Planarity : 0.006 0.049 1955 Dihedral : 15.870 157.389 2354 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.58 % Allowed : 8.31 % Favored : 90.11 % 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 (0.23), residues: 1333 helix: 0.95 (0.20), residues: 674 sheet: -1.21 (0.37), residues: 181 loop : -0.29 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 316 HIS 0.008 0.001 HIS A1325 PHE 0.033 0.002 PHE A 142 TYR 0.029 0.002 TYR A1828 ARG 0.008 0.001 ARG A 86 *********************** 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 200 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 181 time to evaluate : 1.633 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 272 MET cc_start: 0.8028 (mtp) cc_final: 0.7414 (mtp) REVERT: A 307 ARG cc_start: 0.7975 (ttt-90) cc_final: 0.7388 (ttp80) REVERT: A 353 ARG cc_start: 0.7749 (mmm160) cc_final: 0.7409 (mmm160) REVERT: A 371 LYS cc_start: 0.8437 (mttp) cc_final: 0.8234 (tttt) REVERT: A 373 VAL cc_start: 0.3077 (OUTLIER) cc_final: 0.2603 (t) REVERT: A 379 LYS cc_start: 0.8641 (mmtt) cc_final: 0.8134 (mmtt) REVERT: A 503 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7375 (mt-10) REVERT: A 509 ARG cc_start: 0.7763 (mmm160) cc_final: 0.7504 (mmm160) REVERT: A 771 TYR cc_start: 0.1958 (OUTLIER) cc_final: 0.0586 (m-80) REVERT: A 1316 GLU cc_start: 0.5494 (tt0) cc_final: 0.5057 (tm-30) REVERT: A 1323 LEU cc_start: 0.4237 (tp) cc_final: 0.3780 (tt) REVERT: A 1337 ASP cc_start: 0.6699 (OUTLIER) cc_final: 0.4770 (p0) REVERT: A 1354 CYS cc_start: 0.6408 (OUTLIER) cc_final: 0.6087 (m) REVERT: A 1369 MET cc_start: 0.6385 (mpp) cc_final: 0.6044 (mpp) REVERT: A 1661 GLU cc_start: 0.7527 (tp30) cc_final: 0.7324 (tm-30) REVERT: A 1686 TYR cc_start: 0.5554 (t80) cc_final: 0.5191 (t80) REVERT: A 1800 LYS cc_start: 0.7548 (tttp) cc_final: 0.7105 (tptp) REVERT: A 1804 ASP cc_start: 0.6404 (m-30) cc_final: 0.5878 (m-30) REVERT: A 1816 ASP cc_start: 0.3557 (OUTLIER) cc_final: 0.2604 (p0) REVERT: A 1854 MET cc_start: 0.6778 (mmm) cc_final: 0.6529 (mmm) outliers start: 19 outliers final: 13 residues processed: 192 average time/residue: 0.6307 time to fit residues: 167.2594 Evaluate side-chains 183 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 165 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 771 TYR Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 1337 ASP Chi-restraints excluded: chain A residue 1354 CYS Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain A residue 1816 ASP Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 364 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 0.2980 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 A1548 GLN ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4901 moved from start: 0.6186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 12334 Z= 0.262 Angle : 0.616 7.598 16970 Z= 0.326 Chirality : 0.043 0.775 1983 Planarity : 0.005 0.057 1955 Dihedral : 15.871 160.213 2354 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.00 % Allowed : 10.14 % Favored : 87.86 % 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: 0.20 (0.23), residues: 1333 helix: 0.92 (0.20), residues: 678 sheet: -1.12 (0.36), residues: 188 loop : -0.29 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1380 HIS 0.009 0.001 HIS A1683 PHE 0.025 0.002 PHE A1671 TYR 0.024 0.002 TYR A1828 ARG 0.005 0.001 ARG A 459 *********************** 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 215 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 191 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLN cc_start: 0.6613 (OUTLIER) cc_final: 0.6199 (pm20) REVERT: A 272 MET cc_start: 0.8167 (mtp) cc_final: 0.7561 (mtp) REVERT: A 307 ARG cc_start: 0.7829 (ttt-90) cc_final: 0.7619 (ttp80) REVERT: A 379 LYS cc_start: 0.8745 (mmtt) cc_final: 0.8241 (mmtt) REVERT: A 503 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7496 (mt-10) REVERT: A 831 LEU cc_start: 0.5229 (tt) cc_final: 0.5023 (tt) REVERT: A 1316 GLU cc_start: 0.5943 (tt0) cc_final: 0.5500 (tm-30) REVERT: A 1816 ASP cc_start: 0.3379 (OUTLIER) cc_final: 0.2627 (p0) REVERT: A 1854 MET cc_start: 0.6858 (mmm) cc_final: 0.6592 (mmm) outliers start: 24 outliers final: 19 residues processed: 204 average time/residue: 0.6027 time to fit residues: 171.1571 Evaluate side-chains 197 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 176 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1816 ASP Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 364 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 121 optimal weight: 0.0170 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4995 moved from start: 0.6863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12334 Z= 0.187 Angle : 0.539 8.578 16970 Z= 0.286 Chirality : 0.042 0.774 1983 Planarity : 0.005 0.053 1955 Dihedral : 15.792 160.498 2354 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.83 % Allowed : 10.89 % Favored : 86.28 % 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: 0.49 (0.23), residues: 1333 helix: 1.23 (0.20), residues: 683 sheet: -1.12 (0.36), residues: 188 loop : -0.25 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 316 HIS 0.004 0.001 HIS A 356 PHE 0.020 0.001 PHE A 142 TYR 0.018 0.001 TYR A1828 ARG 0.005 0.000 ARG A 789 *********************** 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 218 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 184 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7841 (tttp) REVERT: A 140 GLN cc_start: 0.6597 (OUTLIER) cc_final: 0.6203 (pm20) REVERT: A 272 MET cc_start: 0.8181 (mtp) cc_final: 0.7603 (mtp) REVERT: A 360 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7131 (mm-30) REVERT: A 379 LYS cc_start: 0.8752 (mmtt) cc_final: 0.8272 (mmtt) REVERT: A 503 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7525 (mt-10) REVERT: A 684 MET cc_start: 0.5971 (mpp) cc_final: 0.5643 (mpp) REVERT: A 771 TYR cc_start: 0.3142 (OUTLIER) cc_final: 0.0491 (m-10) REVERT: A 1036 GLU cc_start: 0.7084 (tp30) cc_final: 0.6555 (tp30) REVERT: A 1316 GLU cc_start: 0.5873 (tt0) cc_final: 0.5410 (tm-30) REVERT: A 1337 ASP cc_start: 0.6762 (OUTLIER) cc_final: 0.4854 (p0) REVERT: A 1661 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7291 (tm-30) REVERT: A 1802 MET cc_start: 0.6138 (mmp) cc_final: 0.5919 (mmp) REVERT: A 1816 ASP cc_start: 0.3755 (OUTLIER) cc_final: 0.2880 (p0) REVERT: A 1854 MET cc_start: 0.6932 (mmm) cc_final: 0.6696 (mmm) outliers start: 34 outliers final: 26 residues processed: 207 average time/residue: 0.5884 time to fit residues: 170.4981 Evaluate side-chains 207 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 771 TYR Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1337 ASP Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1580 CYS Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain A residue 1761 HIS Chi-restraints excluded: chain A residue 1816 ASP Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 364 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1299 GLN ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1770 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5486 moved from start: 0.8851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 12334 Z= 0.301 Angle : 0.719 14.093 16970 Z= 0.377 Chirality : 0.046 0.783 1983 Planarity : 0.006 0.066 1955 Dihedral : 16.039 160.673 2354 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.15 % Rotamer: Outliers : 3.08 % Allowed : 11.55 % Favored : 85.37 % 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: -0.36 (0.23), residues: 1333 helix: 0.49 (0.19), residues: 682 sheet: -1.35 (0.34), residues: 204 loop : -0.61 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1380 HIS 0.014 0.002 HIS A1683 PHE 0.029 0.002 PHE A1671 TYR 0.035 0.002 TYR A1828 ARG 0.013 0.001 ARG A1573 *********************** 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 242 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 205 time to evaluate : 1.319 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 83 HIS cc_start: 0.8722 (OUTLIER) cc_final: 0.7851 (p90) REVERT: A 140 GLN cc_start: 0.6912 (OUTLIER) cc_final: 0.6527 (pm20) REVERT: A 217 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6477 (mp0) REVERT: A 268 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8059 (tm-30) REVERT: A 269 ARG cc_start: 0.8732 (ttt180) cc_final: 0.8147 (mtt180) REVERT: A 328 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.5615 (tp30) REVERT: A 359 CYS cc_start: 0.8118 (m) cc_final: 0.7756 (t) REVERT: A 363 PHE cc_start: 0.6431 (m-10) cc_final: 0.5395 (m-10) REVERT: A 379 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8339 (mmtt) REVERT: A 503 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 789 ARG cc_start: 0.7619 (tpp-160) cc_final: 0.7372 (tpp-160) REVERT: A 996 ARG cc_start: 0.6423 (mtm-85) cc_final: 0.6069 (mtm-85) REVERT: A 1316 GLU cc_start: 0.6239 (tt0) cc_final: 0.5784 (tm-30) REVERT: A 1317 MET cc_start: 0.5685 (mtp) cc_final: 0.5042 (mtp) REVERT: A 1356 LEU cc_start: 0.8618 (mt) cc_final: 0.8324 (mt) REVERT: A 1661 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7620 (tm-30) REVERT: A 1727 THR cc_start: 0.6341 (m) cc_final: 0.5047 (t) REVERT: A 1802 MET cc_start: 0.6612 (mmp) cc_final: 0.6401 (mmp) outliers start: 37 outliers final: 33 residues processed: 226 average time/residue: 0.5711 time to fit residues: 182.1510 Evaluate side-chains 230 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 194 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 92 HIS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 790 ARG Chi-restraints excluded: chain A residue 791 LYS Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1337 ASP Chi-restraints excluded: chain A residue 1346 MET Chi-restraints excluded: chain A residue 1545 HIS Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1580 CYS Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1693 ASP Chi-restraints excluded: chain A residue 1748 TYR Chi-restraints excluded: chain A residue 1816 ASP Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 356 GLN Chi-restraints excluded: chain D residue 364 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 75 optimal weight: 0.3980 chunk 134 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 0.2980 chunk 83 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** 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: 0.5431 moved from start: 0.9173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 12334 Z= 0.168 Angle : 0.548 7.886 16970 Z= 0.288 Chirality : 0.042 0.778 1983 Planarity : 0.005 0.060 1955 Dihedral : 15.846 161.375 2354 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.49 % Allowed : 14.38 % Favored : 83.13 % 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: 0.33 (0.24), residues: 1333 helix: 1.16 (0.20), residues: 684 sheet: -1.15 (0.35), residues: 203 loop : -0.42 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 316 HIS 0.005 0.001 HIS A1545 PHE 0.016 0.001 PHE A 142 TYR 0.010 0.001 TYR A 186 ARG 0.003 0.000 ARG A 935 *********************** 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 232 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 202 time to evaluate : 1.697 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 70 LYS cc_start: 0.8569 (mtpt) cc_final: 0.8012 (ttpp) REVERT: A 140 GLN cc_start: 0.6791 (OUTLIER) cc_final: 0.6444 (pm20) REVERT: A 272 MET cc_start: 0.8312 (mtp) cc_final: 0.7743 (mtp) REVERT: A 317 CYS cc_start: 0.6813 (m) cc_final: 0.6596 (m) REVERT: A 359 CYS cc_start: 0.8138 (m) cc_final: 0.7829 (t) REVERT: A 363 PHE cc_start: 0.6259 (m-10) cc_final: 0.5247 (m-10) REVERT: A 379 LYS cc_start: 0.8804 (mmtt) cc_final: 0.8251 (mttm) REVERT: A 503 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7667 (mt-10) REVERT: A 996 ARG cc_start: 0.6294 (mtm-85) cc_final: 0.5945 (mtm-85) REVERT: A 1073 GLN cc_start: 0.6823 (tp40) cc_final: 0.6361 (tp40) REVERT: A 1317 MET cc_start: 0.5882 (mtp) cc_final: 0.5578 (mtp) REVERT: A 1356 LEU cc_start: 0.8657 (mt) cc_final: 0.8440 (mt) REVERT: A 1358 ARG cc_start: 0.7722 (mpt180) cc_final: 0.7372 (tpt170) REVERT: A 1380 TRP cc_start: 0.4975 (t60) cc_final: 0.4132 (t60) REVERT: A 1661 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7634 (tm-30) REVERT: A 1816 ASP cc_start: 0.4576 (OUTLIER) cc_final: 0.2841 (p0) outliers start: 30 outliers final: 26 residues processed: 221 average time/residue: 0.5669 time to fit residues: 173.8401 Evaluate side-chains 227 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 HIS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 791 LYS Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1545 HIS Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1580 CYS Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1687 HIS Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain A residue 1816 ASP Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 356 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5584 moved from start: 0.9845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 12334 Z= 0.204 Angle : 0.571 7.684 16970 Z= 0.303 Chirality : 0.042 0.777 1983 Planarity : 0.005 0.054 1955 Dihedral : 15.849 161.187 2353 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.24 % Allowed : 14.21 % Favored : 82.54 % 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: 0.23 (0.23), residues: 1333 helix: 1.11 (0.20), residues: 682 sheet: -1.15 (0.35), residues: 198 loop : -0.56 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 316 HIS 0.004 0.001 HIS A 356 PHE 0.016 0.002 PHE A1671 TYR 0.018 0.001 TYR A1746 ARG 0.004 0.000 ARG A1060 *********************** 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 242 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 203 time to evaluate : 1.478 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 140 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.6643 (pm20) REVERT: A 272 MET cc_start: 0.8334 (mtp) cc_final: 0.7806 (mtp) REVERT: A 359 CYS cc_start: 0.8106 (m) cc_final: 0.7644 (t) REVERT: A 363 PHE cc_start: 0.6413 (m-10) cc_final: 0.5331 (m-10) REVERT: A 379 LYS cc_start: 0.8815 (mmtt) cc_final: 0.8277 (mttm) REVERT: A 503 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7653 (mt-10) REVERT: A 1036 GLU cc_start: 0.7814 (tp30) cc_final: 0.7388 (tp30) REVERT: A 1073 GLN cc_start: 0.7043 (tp40) cc_final: 0.6666 (tp40) REVERT: A 1317 MET cc_start: 0.6084 (mtp) cc_final: 0.5753 (mtp) REVERT: A 1356 LEU cc_start: 0.8704 (mt) cc_final: 0.8470 (mt) REVERT: A 1358 ARG cc_start: 0.7711 (mpt180) cc_final: 0.7346 (tpt170) REVERT: A 1380 TRP cc_start: 0.5230 (t60) cc_final: 0.4298 (t60) REVERT: A 1585 LYS cc_start: 0.8010 (tmtt) cc_final: 0.7697 (tttp) REVERT: A 1661 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7734 (tm-30) outliers start: 39 outliers final: 35 residues processed: 224 average time/residue: 0.5902 time to fit residues: 184.2715 Evaluate side-chains 233 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 197 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 92 HIS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 790 ARG Chi-restraints excluded: chain A residue 791 LYS Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1346 MET Chi-restraints excluded: chain A residue 1545 HIS Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1580 CYS Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1687 HIS Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain A residue 1761 HIS Chi-restraints excluded: chain A residue 1816 ASP Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 364 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.6980 chunk 125 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 118 optimal weight: 0.0980 chunk 82 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1355 ASN ** 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: 0.5751 moved from start: 1.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 12334 Z= 0.211 Angle : 0.588 7.632 16970 Z= 0.314 Chirality : 0.043 0.781 1983 Planarity : 0.006 0.065 1955 Dihedral : 15.898 161.471 2351 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.97 % Rotamer: Outliers : 2.66 % Allowed : 15.38 % Favored : 81.96 % 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: 1.04 (0.20), residues: 680 sheet: -1.12 (0.36), residues: 196 loop : -0.65 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 316 HIS 0.007 0.001 HIS A1687 PHE 0.015 0.002 PHE A1671 TYR 0.036 0.002 TYR A 936 ARG 0.009 0.001 ARG A 789 *********************** 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 251 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 219 time to evaluate : 1.748 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 70 LYS cc_start: 0.8768 (mtpt) cc_final: 0.8216 (ttpp) REVERT: A 224 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8485 (mp10) REVERT: A 272 MET cc_start: 0.8443 (mtp) cc_final: 0.7779 (mtp) REVERT: A 273 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7574 (mm-30) REVERT: A 316 TRP cc_start: 0.6586 (t60) cc_final: 0.5949 (t60) REVERT: A 328 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.5834 (tp30) REVERT: A 379 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8444 (mmtm) REVERT: A 503 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7644 (mt-10) REVERT: A 637 TYR cc_start: 0.7189 (t80) cc_final: 0.6937 (t80) REVERT: A 812 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8332 (tm-30) REVERT: A 842 MET cc_start: 0.7005 (mmt) cc_final: 0.6739 (mmt) REVERT: A 996 ARG cc_start: 0.7099 (mtm-85) cc_final: 0.6767 (mtm-85) REVERT: A 1073 GLN cc_start: 0.7599 (tp40) cc_final: 0.7142 (tp40) REVERT: A 1355 ASN cc_start: 0.8329 (t0) cc_final: 0.7894 (t0) REVERT: A 1356 LEU cc_start: 0.8760 (mt) cc_final: 0.8458 (mt) REVERT: A 1358 ARG cc_start: 0.7642 (mpt180) cc_final: 0.7275 (tpt170) REVERT: A 1380 TRP cc_start: 0.5540 (t60) cc_final: 0.5148 (t60) REVERT: A 1585 LYS cc_start: 0.8199 (tmtt) cc_final: 0.7881 (tttp) REVERT: A 1661 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7799 (tm-30) REVERT: A 1712 LYS cc_start: 0.7882 (mmmm) cc_final: 0.7661 (mmtp) REVERT: A 1802 MET cc_start: 0.7216 (mmp) cc_final: 0.6685 (mmp) outliers start: 32 outliers final: 30 residues processed: 237 average time/residue: 0.5823 time to fit residues: 192.2739 Evaluate side-chains 242 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 211 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 92 HIS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 791 LYS Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1545 HIS Chi-restraints excluded: chain A residue 1558 CYS Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain A residue 1816 ASP Chi-restraints excluded: chain D residue 352 HIS 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: 1.9990 chunk 92 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 118 optimal weight: 0.0970 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1062 HIS ** 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: 0.5840 moved from start: 1.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 12334 Z= 0.206 Angle : 0.576 9.399 16970 Z= 0.306 Chirality : 0.042 0.780 1983 Planarity : 0.005 0.056 1955 Dihedral : 15.899 161.613 2351 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.33 % Favored : 94.60 % Rotamer: Outliers : 2.83 % Allowed : 16.46 % Favored : 80.71 % 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: 0.04 (0.23), residues: 1333 helix: 0.92 (0.20), residues: 682 sheet: -1.08 (0.36), residues: 201 loop : -0.66 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 316 HIS 0.005 0.001 HIS A 356 PHE 0.018 0.002 PHE A1671 TYR 0.017 0.001 TYR A1828 ARG 0.012 0.001 ARG A 788 ********************** 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 243 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 209 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8795 (mtpt) cc_final: 0.8252 (ttpp) REVERT: A 140 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6813 (pm20) REVERT: A 272 MET cc_start: 0.8483 (mtp) cc_final: 0.7833 (mtp) REVERT: A 273 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7595 (mm-30) REVERT: A 316 TRP cc_start: 0.6816 (t60) cc_final: 0.6074 (t60) REVERT: A 359 CYS cc_start: 0.8066 (m) cc_final: 0.7738 (t) REVERT: A 379 LYS cc_start: 0.8839 (mmtt) cc_final: 0.8463 (mmtm) REVERT: A 503 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7620 (mt-10) REVERT: A 537 PHE cc_start: 0.7076 (OUTLIER) cc_final: 0.6729 (t80) REVERT: A 637 TYR cc_start: 0.7245 (t80) cc_final: 0.6987 (t80) REVERT: A 812 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8354 (tm-30) REVERT: A 842 MET cc_start: 0.6989 (mmt) cc_final: 0.6725 (mmt) REVERT: A 895 LYS cc_start: 0.8382 (mmmm) cc_final: 0.8008 (mmmt) REVERT: A 897 MET cc_start: 0.6850 (mtt) cc_final: 0.6615 (mtt) REVERT: A 996 ARG cc_start: 0.7203 (mtm-85) cc_final: 0.6881 (mtm-85) REVERT: A 1060 ARG cc_start: 0.7578 (tpp80) cc_final: 0.7134 (tpp-160) REVERT: A 1073 GLN cc_start: 0.7800 (tp40) cc_final: 0.7375 (tp40) REVERT: A 1355 ASN cc_start: 0.8316 (t0) cc_final: 0.7843 (t0) REVERT: A 1356 LEU cc_start: 0.8773 (mt) cc_final: 0.8467 (mt) REVERT: A 1358 ARG cc_start: 0.7703 (mpt180) cc_final: 0.7346 (tpt170) REVERT: A 1380 TRP cc_start: 0.5662 (t60) cc_final: 0.5119 (t60) REVERT: A 1585 LYS cc_start: 0.8257 (tmtt) cc_final: 0.7951 (tttp) REVERT: A 1661 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7742 (tm-30) REVERT: A 1692 THR cc_start: 0.7346 (p) cc_final: 0.6835 (t) REVERT: A 1712 LYS cc_start: 0.7945 (mmmm) cc_final: 0.7710 (mmtp) REVERT: A 1802 MET cc_start: 0.7204 (mmp) cc_final: 0.6671 (mmp) REVERT: A 1815 MET cc_start: 0.6831 (tpp) cc_final: 0.6625 (tpp) outliers start: 34 outliers final: 28 residues processed: 229 average time/residue: 0.6025 time to fit residues: 194.4541 Evaluate side-chains 233 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 203 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 92 HIS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 356 HIS Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 791 LYS Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1687 HIS Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain A residue 1816 ASP Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 364 SER 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: 0.0670 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A1062 HIS ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.188494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.150073 restraints weight = 72009.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.158395 restraints weight = 34328.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.163605 restraints weight = 19223.210| |-----------------------------------------------------------------------------| r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 1.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12334 Z= 0.175 Angle : 0.563 8.752 16970 Z= 0.295 Chirality : 0.042 0.779 1983 Planarity : 0.005 0.061 1955 Dihedral : 15.834 161.953 2351 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.16 % Allowed : 17.04 % Favored : 80.80 % 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: 0.28 (0.23), residues: 1333 helix: 1.14 (0.20), residues: 681 sheet: -0.89 (0.37), residues: 196 loop : -0.63 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A1380 HIS 0.012 0.001 HIS A1545 PHE 0.014 0.002 PHE A1671 TYR 0.015 0.001 TYR A1330 ARG 0.007 0.000 ARG A 790 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5849.95 seconds wall clock time: 103 minutes 49.16 seconds (6229.16 seconds total)