Starting phenix.real_space_refine on Sun Sep 13 02:18:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yz4_14387/09_2026/7yz4_14387.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yz4_14387/09_2026/7yz4_14387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yz4_14387/09_2026/7yz4_14387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yz4_14387/09_2026/7yz4_14387.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yz4_14387/09_2026/7yz4_14387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yz4_14387/09_2026/7yz4_14387.map" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.048 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: 5 Type Number sf(0) Gaussians S 55 5.16 5 C 6325 2.51 5 N 1675 2.21 5 O 1797 1.98 5 H 9953 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19805 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 19805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1234, 19805 Classifications: {'peptide': 1234} Link IDs: {'PTRANS': 75, 'TRANS': 1158} Chain breaks: 12 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 2.95, per 1000 atoms: 0.15 Number of scatterers: 19805 At special positions: 0 Unit cell: (97.704, 104.328, 163.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 O 1797 8.00 N 1675 7.00 C 6325 6.00 H 9953 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 496.8 milliseconds 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 12 sheets defined 54.1% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 66 through 81 removed outlier: 3.563A pdb=" N LYS A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.534A pdb=" N ALA A 93 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 117 Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 134 through 144 removed outlier: 3.877A pdb=" N SER A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.738A 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 176 through 182 Processing helix chain 'A' and resid 184 through 195 removed outlier: 4.285A pdb=" N GLU A 188 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 231 removed outlier: 4.936A pdb=" N GLU A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 280 removed outlier: 3.552A pdb=" N PHE A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 313 removed outlier: 4.057A pdb=" N LEU A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 336 removed outlier: 3.652A pdb=" N ALA A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 358 removed outlier: 4.323A pdb=" N LYS A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ILE A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 362 Processing helix chain 'A' and resid 374 through 387 Processing helix chain 'A' and resid 450 through 468 Processing helix chain 'A' and resid 498 through 510 removed outlier: 3.564A pdb=" N GLU A 503 " --> pdb=" O ARG A 499 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 505 " --> pdb=" O GLN A 501 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 506 " --> pdb=" O GLU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 524 removed outlier: 3.889A pdb=" N GLU A 524 " --> pdb=" O VAL A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 521 through 524' Processing helix chain 'A' and resid 542 through 552 removed outlier: 3.827A pdb=" N ARG A 552 " --> pdb=" O GLN A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 591 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 629 through 641 Processing helix chain 'A' and resid 686 through 705 Processing helix chain 'A' and resid 782 through 786 Processing helix chain 'A' and resid 839 through 854 removed outlier: 3.712A pdb=" N PHE A 854 " --> pdb=" O HIS A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 903 removed outlier: 3.592A pdb=" N SER A 903 " --> pdb=" O ASP A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 928 Processing helix chain 'A' and resid 967 through 976 Processing helix chain 'A' and resid 1034 through 1036 No H-bonds generated for 'chain 'A' and resid 1034 through 1036' Processing helix chain 'A' and resid 1044 through 1053 Processing helix chain 'A' and resid 1053 through 1076 removed outlier: 3.634A pdb=" N ILE A1057 " --> pdb=" O CYS A1053 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR A1074 " --> pdb=" O LEU A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1302 Processing helix chain 'A' and resid 1303 through 1307 Processing helix chain 'A' and resid 1312 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 1369 removed outlier: 4.084A pdb=" N MET A1369 " --> pdb=" O PRO A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1570 Processing helix chain 'A' and resid 1571 through 1583 removed outlier: 3.504A pdb=" N GLY A1583 " --> pdb=" O LEU A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1650 through 1658 Processing helix chain 'A' and resid 1662 through 1667 Processing helix chain 'A' and resid 1674 through 1681 removed outlier: 3.673A pdb=" N LEU A1678 " --> pdb=" O LYS A1674 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1716 removed outlier: 3.644A pdb=" N LEU A1701 " --> pdb=" O ARG A1697 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA A1704 " --> pdb=" O PHE A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1734 Processing helix chain 'A' and resid 1735 through 1746 Processing helix chain 'A' and resid 1747 through 1752 Processing helix chain 'A' and resid 1756 through 1773 Processing helix chain 'A' and resid 1799 through 1816 removed outlier: 4.106A pdb=" N GLY A1803 " --> pdb=" O PRO A1799 " (cutoff:3.500A) Processing helix chain 'A' and resid 1821 through 1842 Proline residue: A1830 - end of helix Proline residue: A1834 - end of helix Processing helix chain 'A' and resid 1846 through 1855 Processing helix chain 'A' and resid 1890 through 1910 Processing sheet with id=AA1, first strand: chain 'A' and resid 205 through 206 removed outlier: 7.712A pdb=" N THR A 206 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 62 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.804A pdb=" N THR A 151 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG A 95 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU A 171 " --> pdb=" O ARG A 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 257 removed outlier: 6.152A pdb=" N VAL A 534 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU A 563 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 446 through 448 removed outlier: 5.716A pdb=" N ILE A 446 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN A 477 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N THR A 519 " --> pdb=" O ASN A 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 666 through 667 Processing sheet with id=AA6, first strand: chain 'A' and resid 746 through 750 removed outlier: 3.587A pdb=" N GLN A 747 " --> pdb=" O ILE A1550 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 777 through 780 removed outlier: 6.469A pdb=" N GLU A 824 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 777 through 780 removed outlier: 6.469A pdb=" N GLU A 824 " --> pdb=" O THR A 778 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ILE A 829 " --> pdb=" O GLY A 774 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY A 774 " --> pdb=" O ILE A 829 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU A 831 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL A 772 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS A 833 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N PHE A 802 " --> pdb=" O ILE A 773 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N CYS A 877 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 865 through 867 removed outlier: 3.503A pdb=" N VAL A1386 " --> pdb=" O GLU A 866 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 987 through 992 removed outlier: 3.574A pdb=" N LEU A 987 " --> pdb=" O TYR A 951 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP A 949 " --> pdb=" O ASP A 989 " (cutoff:3.500A) removed outlier: 6.771A 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=AB2, first strand: chain 'A' and resid 1859 through 1861 Processing sheet with id=AB3, first strand: chain 'A' and resid 1859 through 1861 492 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.30 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9919 1.03 - 1.23: 38 1.23 - 1.43: 4101 1.43 - 1.62: 5885 1.62 - 1.82: 76 Bond restraints: 20019 Sorted by residual: bond pdb=" CG LEU A1312 " pdb=" CD1 LEU A1312 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.94e+00 bond pdb=" ND2 ASN A1311 " pdb="HD22 ASN A1311 " ideal model delta sigma weight residual 0.860 0.832 0.028 2.00e-02 2.50e+03 1.93e+00 bond pdb=" CB LEU A1312 " pdb=" CG LEU A1312 " ideal model delta sigma weight residual 1.530 1.502 0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C ALA A 555 " pdb=" N PRO A 556 " ideal model delta sigma weight residual 1.334 1.354 -0.020 1.51e-02 4.39e+03 1.70e+00 bond pdb=" ND2 ASN A 161 " pdb="HD22 ASN A 161 " ideal model delta sigma weight residual 0.860 0.835 0.025 2.00e-02 2.50e+03 1.54e+00 ... (remaining 20014 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.54: 36293 7.54 - 15.07: 2 15.07 - 22.61: 0 22.61 - 30.15: 1 30.15 - 37.69: 2 Bond angle restraints: 36298 Sorted by residual: angle pdb=" N ASP A1764 " pdb=" CA ASP A1764 " pdb=" HA ASP A1764 " ideal model delta sigma weight residual 110.00 72.31 37.69 3.00e+00 1.11e-01 1.58e+02 angle pdb=" CB ASP A1764 " pdb=" CA ASP A1764 " pdb=" HA ASP A1764 " ideal model delta sigma weight residual 109.00 73.25 35.75 3.00e+00 1.11e-01 1.42e+02 angle pdb=" C ASP A1764 " pdb=" CA ASP A1764 " pdb=" HA ASP A1764 " ideal model delta sigma weight residual 109.00 78.99 30.01 3.00e+00 1.11e-01 1.00e+02 angle pdb=" N LEU A 313 " pdb=" CA LEU A 313 " pdb=" C LEU A 313 " ideal model delta sigma weight residual 107.73 115.46 -7.73 1.34e+00 5.57e-01 3.32e+01 angle pdb=" N GLU A1313 " pdb=" CA GLU A1313 " pdb=" C GLU A1313 " ideal model delta sigma weight residual 111.37 117.30 -5.93 1.65e+00 3.67e-01 1.29e+01 ... (remaining 36293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 8728 17.19 - 34.37: 519 34.37 - 51.56: 152 51.56 - 68.74: 35 68.74 - 85.93: 9 Dihedral angle restraints: 9443 sinusoidal: 5179 harmonic: 4264 Sorted by residual: dihedral pdb=" N ASP A1764 " pdb=" C ASP A1764 " pdb=" CA ASP A1764 " pdb=" CB ASP A1764 " ideal model delta harmonic sigma weight residual 122.80 131.36 -8.56 0 2.50e+00 1.60e-01 1.17e+01 dihedral pdb=" C ASP A1764 " pdb=" N ASP A1764 " pdb=" CA ASP A1764 " pdb=" CB ASP A1764 " ideal model delta harmonic sigma weight residual -122.60 -130.83 8.23 0 2.50e+00 1.60e-01 1.08e+01 dihedral pdb=" CG ARG A 269 " pdb=" CD ARG A 269 " pdb=" NE ARG A 269 " pdb=" CZ ARG A 269 " ideal model delta sinusoidal sigma weight residual -90.00 -133.47 43.47 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 9440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1340 0.065 - 0.130: 193 0.130 - 0.195: 17 0.195 - 0.261: 1 0.261 - 0.326: 1 Chirality restraints: 1552 Sorted by residual: chirality pdb=" CA ASP A1764 " pdb=" N ASP A1764 " pdb=" C ASP A1764 " pdb=" CB ASP A1764 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA HIS A1655 " pdb=" N HIS A1655 " pdb=" C HIS A1655 " pdb=" CB HIS A1655 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE A 479 " pdb=" N ILE A 479 " pdb=" C ILE A 479 " pdb=" CB ILE A 479 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.13e-01 ... (remaining 1549 not shown) Planarity restraints: 2880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1311 " -0.052 2.00e-02 2.50e+03 6.82e-02 6.97e+01 pdb=" CG ASN A1311 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN A1311 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A1311 " 0.111 2.00e-02 2.50e+03 pdb="HD21 ASN A1311 " 0.007 2.00e-02 2.50e+03 pdb="HD22 ASN A1311 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 161 " 0.047 2.00e-02 2.50e+03 6.37e-02 6.08e+01 pdb=" CG ASN A 161 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 161 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 161 " -0.104 2.00e-02 2.50e+03 pdb="HD21 ASN A 161 " -0.011 2.00e-02 2.50e+03 pdb="HD22 ASN A 161 " 0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 985 " -0.040 2.00e-02 2.50e+03 5.12e-02 3.93e+01 pdb=" CD GLN A 985 " 0.030 2.00e-02 2.50e+03 pdb=" OE1 GLN A 985 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN A 985 " 0.083 2.00e-02 2.50e+03 pdb="HE21 GLN A 985 " 0.003 2.00e-02 2.50e+03 pdb="HE22 GLN A 985 " -0.079 2.00e-02 2.50e+03 ... (remaining 2877 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1475 2.23 - 2.82: 44609 2.82 - 3.42: 50832 3.42 - 4.01: 66736 4.01 - 4.60: 104009 Nonbonded interactions: 267661 Sorted by model distance: nonbonded pdb="HE22 GLN A1679 " pdb=" OD1 ASP A1693 " model vdw 1.641 2.450 nonbonded pdb=" HG1 THR A1867 " pdb=" OD1 ASP A1869 " model vdw 1.669 2.450 nonbonded pdb=" O GLU A 542 " pdb=" HG SER A 545 " model vdw 1.683 2.450 nonbonded pdb=" HA ASP A1764 " pdb=" HB3 ASP A1764 " model vdw 1.683 1.952 nonbonded pdb=" OD2 ASP A 319 " pdb=" HH TYR A 362 " model vdw 1.686 2.450 ... (remaining 267656 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: 5.470 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: 0.110 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.860 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 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 0.046 10066 Z= 0.188 Angle : 0.780 9.299 13634 Z= 0.425 Chirality : 0.046 0.326 1552 Planarity : 0.009 0.123 1732 Dihedral : 11.946 85.927 3798 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.92 % Allowed : 6.98 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.22), residues: 1208 helix: -0.99 (0.19), residues: 598 sheet: -1.46 (0.47), residues: 135 loop : -1.78 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.003 ARG A 790 TYR 0.032 0.003 TYR A1695 PHE 0.030 0.003 PHE A1700 TRP 0.027 0.005 TRP A 133 HIS 0.013 0.002 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (10066) covalent geometry : angle 0.78015 / 0.43 (13634) hydrogen bonds : bond 0.15257 / 10.67 ( 489) hydrogen bonds : angle 6.07495 / 4.42 ( 1398) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue THR 655 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue ILE 907 is missing expected H atoms. Skipping. Residue ILE 909 is missing expected H atoms. Skipping. Residue SER 911 is missing expected H atoms. Skipping. Residue THR 912 is missing expected H atoms. Skipping. Residue LYS 913 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue SER 915 is missing expected H atoms. Skipping. Residue LYS 916 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 210 time to evaluate : 0.500 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: A 53 GLU cc_start: 0.6977 (tp30) cc_final: 0.6621 (tt0) REVERT: A 144 LYS cc_start: 0.8235 (mttt) cc_final: 0.7962 (mttp) REVERT: A 193 CYS cc_start: 0.7425 (t) cc_final: 0.7103 (t) REVERT: A 219 LEU cc_start: 0.8013 (tp) cc_final: 0.7778 (tp) REVERT: A 222 LYS cc_start: 0.7640 (mmtt) cc_final: 0.7427 (ttpt) REVERT: A 225 LYS cc_start: 0.8157 (tttp) cc_final: 0.7956 (tttt) REVERT: A 307 ARG cc_start: 0.7995 (ptp-110) cc_final: 0.7678 (ptp-110) REVERT: A 324 MET cc_start: 0.6767 (mpp) cc_final: 0.6320 (tpp) REVERT: A 325 MET cc_start: 0.7579 (mtt) cc_final: 0.7274 (mtt) REVERT: A 477 ASN cc_start: 0.7991 (t0) cc_final: 0.7292 (m-40) REVERT: A 546 TYR cc_start: 0.8037 (t80) cc_final: 0.7762 (t80) REVERT: A 578 THR cc_start: 0.8371 (m) cc_final: 0.8133 (p) REVERT: A 771 TYR cc_start: 0.6920 (m-80) cc_final: 0.6390 (m-80) REVERT: A 791 LYS cc_start: 0.8417 (pttt) cc_final: 0.7967 (ptmm) REVERT: A 851 GLN cc_start: 0.7235 (pt0) cc_final: 0.6847 (pt0) REVERT: A 1066 THR cc_start: 0.7757 (m) cc_final: 0.7475 (p) REVERT: A 1345 TYR cc_start: 0.6926 (t80) cc_final: 0.6710 (t80) REVERT: A 1768 LYS cc_start: 0.7039 (mttt) cc_final: 0.6706 (mmmt) outliers start: 10 outliers final: 3 residues processed: 217 average time/residue: 0.2804 time to fit residues: 79.5738 Evaluate side-chains 169 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 166 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 1372 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 HIS A 184 HIS A 356 HIS A 985 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.197290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.166490 restraints weight = 52418.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.172370 restraints weight = 23085.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.175980 restraints weight = 13062.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.178209 restraints weight = 8869.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.179068 restraints weight = 6899.241| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10066 Z= 0.176 Angle : 0.585 5.329 13634 Z= 0.312 Chirality : 0.041 0.325 1552 Planarity : 0.005 0.050 1732 Dihedral : 4.022 34.575 1355 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.83 % Allowed : 10.19 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.23), residues: 1208 helix: 0.33 (0.20), residues: 603 sheet: -1.14 (0.49), residues: 131 loop : -1.25 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 137 TYR 0.020 0.001 TYR A1335 PHE 0.023 0.001 PHE A1700 TRP 0.014 0.002 TRP A 316 HIS 0.007 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (10066) covalent geometry : angle 0.58485 / 0.31 (13634) hydrogen bonds : bond 0.04950 / 3.37 ( 489) hydrogen bonds : angle 4.84009 / 3.55 ( 1398) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue THR 655 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue ILE 907 is missing expected H atoms. Skipping. Residue ILE 909 is missing expected H atoms. Skipping. Residue SER 911 is missing expected H atoms. Skipping. Residue THR 912 is missing expected H atoms. Skipping. Residue LYS 913 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue SER 915 is missing expected H atoms. Skipping. Residue LYS 916 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 167 time to evaluate : 0.512 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: A 137 ARG cc_start: 0.6529 (ptm160) cc_final: 0.6261 (ptm160) REVERT: A 307 ARG cc_start: 0.8056 (ptp-110) cc_final: 0.7787 (ptp-110) REVERT: A 325 MET cc_start: 0.7225 (mtt) cc_final: 0.7020 (mtt) REVERT: A 477 ASN cc_start: 0.8003 (t0) cc_final: 0.7439 (m-40) REVERT: A 771 TYR cc_start: 0.7248 (m-80) cc_final: 0.6600 (m-80) REVERT: A 791 LYS cc_start: 0.8408 (pttt) cc_final: 0.8099 (ptmm) REVERT: A 851 GLN cc_start: 0.7332 (pt0) cc_final: 0.7051 (pt0) REVERT: A 1066 THR cc_start: 0.7772 (m) cc_final: 0.7516 (p) REVERT: A 1345 TYR cc_start: 0.7061 (t80) cc_final: 0.6739 (t80) REVERT: A 1547 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6702 (mt-10) REVERT: A 1746 TYR cc_start: 0.7615 (m-80) cc_final: 0.7394 (m-80) REVERT: A 1768 LYS cc_start: 0.6977 (mttt) cc_final: 0.6678 (mmmt) outliers start: 9 outliers final: 6 residues processed: 172 average time/residue: 0.2778 time to fit residues: 63.3118 Evaluate side-chains 167 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 161 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 1657 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 39 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 18 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 72.0878 > 50:) chunk 80 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 92 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 ASN A 356 HIS A 458 ASN A1339 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.197982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.167926 restraints weight = 52205.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.173756 restraints weight = 22858.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.177353 restraints weight = 12797.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.179434 restraints weight = 8590.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.180810 restraints weight = 6709.495| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6159 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10066 Z= 0.112 Angle : 0.514 4.928 13634 Z= 0.264 Chirality : 0.039 0.317 1552 Planarity : 0.004 0.047 1732 Dihedral : 3.840 36.360 1354 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.10 % Allowed : 10.65 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.24), residues: 1208 helix: 0.87 (0.21), residues: 602 sheet: -1.08 (0.48), residues: 133 loop : -0.93 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 746 TYR 0.013 0.001 TYR A 47 PHE 0.012 0.001 PHE A1700 TRP 0.013 0.002 TRP A 133 HIS 0.004 0.001 HIS A1683 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (10066) covalent geometry : angle 0.51444 / 0.26 (13634) hydrogen bonds : bond 0.04095 / 2.77 ( 489) hydrogen bonds : angle 4.41788 / 3.24 ( 1398) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue THR 655 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue ILE 907 is missing expected H atoms. Skipping. Residue ILE 909 is missing expected H atoms. Skipping. Residue SER 911 is missing expected H atoms. Skipping. Residue THR 912 is missing expected H atoms. Skipping. Residue LYS 913 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue SER 915 is missing expected H atoms. Skipping. Residue LYS 916 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.556 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: A 60 THR cc_start: 0.7715 (t) cc_final: 0.7500 (p) REVERT: A 137 ARG cc_start: 0.6579 (ptm160) cc_final: 0.6040 (ptm160) REVERT: A 325 MET cc_start: 0.7183 (mtt) cc_final: 0.6956 (mtt) REVERT: A 354 LYS cc_start: 0.7286 (mtpt) cc_final: 0.6979 (mtpp) REVERT: A 477 ASN cc_start: 0.7832 (t0) cc_final: 0.7192 (m-40) REVERT: A 478 PHE cc_start: 0.7492 (p90) cc_final: 0.6691 (p90) REVERT: A 546 TYR cc_start: 0.8016 (t80) cc_final: 0.7587 (t80) REVERT: A 791 LYS cc_start: 0.8420 (pttt) cc_final: 0.8114 (ptmm) REVERT: A 1066 THR cc_start: 0.7699 (m) cc_final: 0.7393 (p) REVERT: A 1345 TYR cc_start: 0.7029 (t80) cc_final: 0.6732 (t80) REVERT: A 1547 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6700 (mt-10) REVERT: A 1661 GLU cc_start: 0.5617 (pm20) cc_final: 0.4833 (pm20) REVERT: A 1768 LYS cc_start: 0.7025 (mttt) cc_final: 0.6678 (mmmt) outliers start: 12 outliers final: 9 residues processed: 169 average time/residue: 0.2708 time to fit residues: 60.1385 Evaluate side-chains 168 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 1310 PHE Chi-restraints excluded: chain A residue 1657 ILE Chi-restraints excluded: chain A residue 1682 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 18 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 117 optimal weight: 20.0000 chunk 75 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 37 optimal weight: 0.0060 chunk 77 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 356 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.197088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.166789 restraints weight = 52617.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.172793 restraints weight = 23060.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.176220 restraints weight = 12838.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.178543 restraints weight = 8716.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.179487 restraints weight = 6767.165| |-----------------------------------------------------------------------------| r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10066 Z= 0.124 Angle : 0.508 4.924 13634 Z= 0.263 Chirality : 0.039 0.322 1552 Planarity : 0.004 0.060 1732 Dihedral : 3.804 36.108 1354 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.10 % Allowed : 11.02 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.24), residues: 1208 helix: 1.11 (0.21), residues: 601 sheet: -1.03 (0.46), residues: 136 loop : -0.84 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 746 TYR 0.021 0.001 TYR A1335 PHE 0.012 0.001 PHE A1700 TRP 0.019 0.002 TRP A 133 HIS 0.004 0.001 HIS A1655 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (10066) covalent geometry : angle 0.50764 / 0.26 (13634) hydrogen bonds : bond 0.03960 / 2.67 ( 489) hydrogen bonds : angle 4.34315 / 3.19 ( 1398) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue THR 655 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue ILE 907 is missing expected H atoms. Skipping. Residue ILE 909 is missing expected H atoms. Skipping. Residue SER 911 is missing expected H atoms. Skipping. Residue THR 912 is missing expected H atoms. Skipping. Residue LYS 913 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue SER 915 is missing expected H atoms. Skipping. Residue LYS 916 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.544 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: A 191 LYS cc_start: 0.8148 (tptt) cc_final: 0.7915 (tptt) REVERT: A 354 LYS cc_start: 0.7250 (mtpt) cc_final: 0.6909 (mtpp) REVERT: A 477 ASN cc_start: 0.7779 (t0) cc_final: 0.7394 (m-40) REVERT: A 478 PHE cc_start: 0.7460 (p90) cc_final: 0.6705 (p90) REVERT: A 791 LYS cc_start: 0.8413 (pttt) cc_final: 0.8113 (ptmm) REVERT: A 1066 THR cc_start: 0.7738 (m) cc_final: 0.7405 (p) REVERT: A 1345 TYR cc_start: 0.7049 (t80) cc_final: 0.6737 (t80) REVERT: A 1547 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6711 (mt-10) REVERT: A 1661 GLU cc_start: 0.5275 (pm20) cc_final: 0.4564 (pm20) REVERT: A 1768 LYS cc_start: 0.6994 (mttt) cc_final: 0.6674 (mmmt) outliers start: 12 outliers final: 10 residues processed: 172 average time/residue: 0.2773 time to fit residues: 62.8729 Evaluate side-chains 163 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 1310 PHE Chi-restraints excluded: chain A residue 1657 ILE Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1692 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 27 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 ASN A 356 HIS A 458 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.195351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.164955 restraints weight = 52089.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.170827 restraints weight = 23203.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.174405 restraints weight = 13051.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.176458 restraints weight = 8847.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.177891 restraints weight = 6949.780| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10066 Z= 0.149 Angle : 0.523 5.301 13634 Z= 0.273 Chirality : 0.040 0.325 1552 Planarity : 0.004 0.064 1732 Dihedral : 3.888 36.622 1354 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.29 % Allowed : 11.66 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.25), residues: 1208 helix: 1.17 (0.21), residues: 604 sheet: -0.87 (0.45), residues: 141 loop : -0.69 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 269 TYR 0.011 0.001 TYR A 546 PHE 0.014 0.001 PHE A1700 TRP 0.024 0.002 TRP A 133 HIS 0.006 0.001 HIS A1655 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (10066) covalent geometry : angle 0.52308 / 0.27 (13634) hydrogen bonds : bond 0.04080 / 2.75 ( 489) hydrogen bonds : angle 4.33572 / 3.19 ( 1398) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue THR 655 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue ILE 907 is missing expected H atoms. Skipping. Residue ILE 909 is missing expected H atoms. Skipping. Residue SER 911 is missing expected H atoms. Skipping. Residue THR 912 is missing expected H atoms. Skipping. Residue LYS 913 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue SER 915 is missing expected H atoms. Skipping. Residue LYS 916 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.531 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: A 101 ASN cc_start: 0.8209 (p0) cc_final: 0.7831 (p0) REVERT: A 477 ASN cc_start: 0.8076 (t0) cc_final: 0.7636 (m110) REVERT: A 1066 THR cc_start: 0.7688 (m) cc_final: 0.7348 (p) REVERT: A 1345 TYR cc_start: 0.7110 (t80) cc_final: 0.6768 (t80) REVERT: A 1547 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6687 (mt-10) REVERT: A 1661 GLU cc_start: 0.4676 (pm20) cc_final: 0.3796 (pm20) REVERT: A 1768 LYS cc_start: 0.7049 (mttt) cc_final: 0.6706 (mmmt) outliers start: 14 outliers final: 9 residues processed: 160 average time/residue: 0.2603 time to fit residues: 55.4855 Evaluate side-chains 159 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 1310 PHE Chi-restraints excluded: chain A residue 1657 ILE Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1692 THR Chi-restraints excluded: chain A residue 1808 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 118 optimal weight: 0.0570 chunk 67 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.195477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.164626 restraints weight = 52210.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.170540 restraints weight = 23420.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.174185 restraints weight = 13252.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.176014 restraints weight = 8991.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.177633 restraints weight = 7189.040| |-----------------------------------------------------------------------------| r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10066 Z= 0.142 Angle : 0.520 5.865 13634 Z= 0.268 Chirality : 0.040 0.321 1552 Planarity : 0.005 0.065 1732 Dihedral : 3.836 37.448 1353 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.84 % Allowed : 11.75 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.25), residues: 1208 helix: 1.26 (0.21), residues: 604 sheet: -0.81 (0.46), residues: 141 loop : -0.63 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1719 TYR 0.016 0.001 TYR A 927 PHE 0.011 0.001 PHE A1700 TRP 0.012 0.001 TRP A 133 HIS 0.008 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (10066) covalent geometry : angle 0.52009 / 0.27 (13634) hydrogen bonds : bond 0.03963 / 2.67 ( 489) hydrogen bonds : angle 4.26144 / 3.14 ( 1398) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue THR 655 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue ILE 907 is missing expected H atoms. Skipping. Residue ILE 909 is missing expected H atoms. Skipping. Residue SER 911 is missing expected H atoms. Skipping. Residue THR 912 is missing expected H atoms. Skipping. Residue LYS 913 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue SER 915 is missing expected H atoms. Skipping. Residue LYS 916 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.508 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: A 304 SER cc_start: 0.8780 (t) cc_final: 0.8560 (p) REVERT: A 543 TYR cc_start: 0.7339 (t80) cc_final: 0.7064 (t80) REVERT: A 746 ARG cc_start: 0.6614 (ppt170) cc_final: 0.6404 (ppt170) REVERT: A 1066 THR cc_start: 0.7696 (m) cc_final: 0.7432 (p) REVERT: A 1345 TYR cc_start: 0.7145 (t80) cc_final: 0.6776 (t80) REVERT: A 1547 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6669 (mt-10) REVERT: A 1661 GLU cc_start: 0.4299 (pm20) cc_final: 0.3426 (pm20) REVERT: A 1768 LYS cc_start: 0.7050 (mttt) cc_final: 0.6708 (mmmt) outliers start: 20 outliers final: 16 residues processed: 165 average time/residue: 0.2710 time to fit residues: 59.4644 Evaluate side-chains 162 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 451 ARG Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 1310 PHE Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1577 LEU Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1692 THR Chi-restraints excluded: chain A residue 1808 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1683 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.194191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.163228 restraints weight = 52926.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.169003 restraints weight = 23715.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.172684 restraints weight = 13545.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.174704 restraints weight = 9191.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.175671 restraints weight = 7247.466| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10066 Z= 0.163 Angle : 0.527 4.932 13634 Z= 0.276 Chirality : 0.040 0.325 1552 Planarity : 0.005 0.064 1732 Dihedral : 3.904 37.632 1353 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.84 % Allowed : 11.48 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.25), residues: 1208 helix: 1.21 (0.21), residues: 604 sheet: -0.84 (0.46), residues: 140 loop : -0.62 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 187 TYR 0.011 0.001 TYR A1695 PHE 0.013 0.001 PHE A1700 TRP 0.011 0.001 TRP A 316 HIS 0.013 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (10066) covalent geometry : angle 0.52652 / 0.28 (13634) hydrogen bonds : bond 0.04122 / 2.77 ( 489) hydrogen bonds : angle 4.29983 / 3.17 ( 1398) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue THR 655 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue ILE 907 is missing expected H atoms. Skipping. Residue ILE 909 is missing expected H atoms. Skipping. Residue SER 911 is missing expected H atoms. Skipping. Residue THR 912 is missing expected H atoms. Skipping. Residue LYS 913 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue SER 915 is missing expected H atoms. Skipping. Residue LYS 916 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.512 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: A 304 SER cc_start: 0.8821 (t) cc_final: 0.8604 (p) REVERT: A 354 LYS cc_start: 0.7401 (mttt) cc_final: 0.7074 (mttm) REVERT: A 359 CYS cc_start: 0.8184 (m) cc_final: 0.7971 (m) REVERT: A 746 ARG cc_start: 0.6899 (ppt170) cc_final: 0.6137 (ppt170) REVERT: A 1066 THR cc_start: 0.7653 (m) cc_final: 0.7391 (p) REVERT: A 1345 TYR cc_start: 0.7128 (t80) cc_final: 0.6748 (t80) REVERT: A 1547 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6731 (mt-10) REVERT: A 1661 GLU cc_start: 0.4333 (pm20) cc_final: 0.3656 (pm20) REVERT: A 1768 LYS cc_start: 0.7106 (mttt) cc_final: 0.6771 (mmmt) outliers start: 20 outliers final: 17 residues processed: 170 average time/residue: 0.2764 time to fit residues: 62.6579 Evaluate side-chains 168 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 451 ARG Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 1310 PHE Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1692 THR Chi-restraints excluded: chain A residue 1747 ASP Chi-restraints excluded: chain A residue 1808 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 35 optimal weight: 0.2980 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 105 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.195685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.165005 restraints weight = 52293.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.170917 restraints weight = 23411.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.174569 restraints weight = 13291.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.176597 restraints weight = 8979.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.177460 restraints weight = 7089.220| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6240 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10066 Z= 0.119 Angle : 0.514 5.607 13634 Z= 0.263 Chirality : 0.039 0.317 1552 Planarity : 0.005 0.064 1732 Dihedral : 3.840 37.617 1353 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.56 % Allowed : 12.67 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.25), residues: 1208 helix: 1.36 (0.21), residues: 604 sheet: -0.78 (0.46), residues: 140 loop : -0.52 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1719 TYR 0.012 0.001 TYR A 543 PHE 0.010 0.001 PHE A1700 TRP 0.034 0.002 TRP A 133 HIS 0.014 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (10066) covalent geometry : angle 0.51378 / 0.26 (13634) hydrogen bonds : bond 0.03729 / 2.49 ( 489) hydrogen bonds : angle 4.14448 / 3.06 ( 1398) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue THR 655 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue ILE 907 is missing expected H atoms. Skipping. Residue ILE 909 is missing expected H atoms. Skipping. Residue SER 911 is missing expected H atoms. Skipping. Residue THR 912 is missing expected H atoms. Skipping. Residue LYS 913 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue SER 915 is missing expected H atoms. Skipping. Residue LYS 916 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.523 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: A 304 SER cc_start: 0.8800 (t) cc_final: 0.8598 (p) REVERT: A 354 LYS cc_start: 0.7256 (mttt) cc_final: 0.6889 (mttm) REVERT: A 359 CYS cc_start: 0.8136 (m) cc_final: 0.7256 (p) REVERT: A 537 PHE cc_start: 0.7400 (m-80) cc_final: 0.7157 (m-80) REVERT: A 577 LYS cc_start: 0.8812 (mttt) cc_final: 0.8524 (mttp) REVERT: A 746 ARG cc_start: 0.6967 (ppt170) cc_final: 0.6109 (ppt170) REVERT: A 1066 THR cc_start: 0.7644 (m) cc_final: 0.7386 (p) REVERT: A 1345 TYR cc_start: 0.7144 (t80) cc_final: 0.6727 (t80) REVERT: A 1661 GLU cc_start: 0.4272 (pm20) cc_final: 0.3560 (pm20) REVERT: A 1768 LYS cc_start: 0.7073 (mttt) cc_final: 0.6731 (mmmt) outliers start: 17 outliers final: 14 residues processed: 170 average time/residue: 0.2748 time to fit residues: 61.9375 Evaluate side-chains 170 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 451 ARG Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 1310 PHE Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1692 THR Chi-restraints excluded: chain A residue 1808 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 56 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 356 HIS ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.193792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.162850 restraints weight = 52134.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.168702 restraints weight = 23614.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.172338 restraints weight = 13536.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.174582 restraints weight = 9205.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.175863 restraints weight = 7154.754| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10066 Z= 0.169 Angle : 0.539 4.932 13634 Z= 0.283 Chirality : 0.040 0.326 1552 Planarity : 0.005 0.062 1732 Dihedral : 3.945 37.493 1353 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.38 % Allowed : 13.13 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.25), residues: 1208 helix: 1.25 (0.21), residues: 604 sheet: -0.87 (0.46), residues: 140 loop : -0.48 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 187 TYR 0.012 0.001 TYR A1695 PHE 0.012 0.001 PHE A1700 TRP 0.041 0.003 TRP A 133 HIS 0.014 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (10066) covalent geometry : angle 0.53892 / 0.28 (13634) hydrogen bonds : bond 0.04136 / 2.78 ( 489) hydrogen bonds : angle 4.30974 / 3.17 ( 1398) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue THR 655 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue ILE 907 is missing expected H atoms. Skipping. Residue ILE 909 is missing expected H atoms. Skipping. Residue SER 911 is missing expected H atoms. Skipping. Residue THR 912 is missing expected H atoms. Skipping. Residue LYS 913 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue SER 915 is missing expected H atoms. Skipping. Residue LYS 916 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.503 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: A 133 TRP cc_start: 0.7006 (m100) cc_final: 0.6798 (m100) REVERT: A 359 CYS cc_start: 0.8241 (m) cc_final: 0.7375 (p) REVERT: A 577 LYS cc_start: 0.8811 (mttt) cc_final: 0.8541 (mttp) REVERT: A 746 ARG cc_start: 0.7022 (ppt170) cc_final: 0.6164 (ppt170) REVERT: A 851 GLN cc_start: 0.7343 (pt0) cc_final: 0.7013 (pt0) REVERT: A 1066 THR cc_start: 0.7683 (m) cc_final: 0.7415 (p) REVERT: A 1345 TYR cc_start: 0.7144 (t80) cc_final: 0.6740 (t80) REVERT: A 1661 GLU cc_start: 0.4417 (pm20) cc_final: 0.3962 (pm20) REVERT: A 1768 LYS cc_start: 0.7125 (mttt) cc_final: 0.6778 (mmmt) outliers start: 15 outliers final: 15 residues processed: 170 average time/residue: 0.2829 time to fit residues: 63.2889 Evaluate side-chains 170 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 451 ARG Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 1310 PHE Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1692 THR Chi-restraints excluded: chain A residue 1808 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.196665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.163169 restraints weight = 51389.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.169066 restraints weight = 23997.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.172691 restraints weight = 14217.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.174961 restraints weight = 10005.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.176264 restraints weight = 7945.060| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10066 Z= 0.224 Angle : 0.582 5.106 13634 Z= 0.314 Chirality : 0.042 0.331 1552 Planarity : 0.005 0.062 1732 Dihedral : 4.200 37.612 1353 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.56 % Allowed : 12.95 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.25), residues: 1208 helix: 0.98 (0.21), residues: 604 sheet: -1.03 (0.46), residues: 138 loop : -0.55 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 187 TYR 0.015 0.001 TYR A1695 PHE 0.016 0.001 PHE A1681 TRP 0.037 0.003 TRP A 133 HIS 0.014 0.002 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 (10066) covalent geometry : angle 0.58198 / 0.31 (13634) hydrogen bonds : bond 0.04671 / 3.11 ( 489) hydrogen bonds : angle 4.57185 / 3.37 ( 1398) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue THR 655 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue ILE 907 is missing expected H atoms. Skipping. Residue ILE 909 is missing expected H atoms. Skipping. Residue SER 911 is missing expected H atoms. Skipping. Residue THR 912 is missing expected H atoms. Skipping. Residue LYS 913 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue SER 915 is missing expected H atoms. Skipping. Residue LYS 916 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.348 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: A 359 CYS cc_start: 0.8225 (m) cc_final: 0.7400 (p) REVERT: A 577 LYS cc_start: 0.8864 (mttt) cc_final: 0.8593 (mttp) REVERT: A 746 ARG cc_start: 0.7089 (ppt170) cc_final: 0.6138 (ppt170) REVERT: A 851 GLN cc_start: 0.7328 (pt0) cc_final: 0.6989 (pt0) REVERT: A 1066 THR cc_start: 0.7693 (m) cc_final: 0.7430 (p) REVERT: A 1345 TYR cc_start: 0.7175 (t80) cc_final: 0.6732 (t80) REVERT: A 1547 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6730 (mt-10) REVERT: A 1661 GLU cc_start: 0.4583 (pm20) cc_final: 0.4321 (pm20) REVERT: A 1768 LYS cc_start: 0.7330 (mttt) cc_final: 0.7125 (tppt) outliers start: 17 outliers final: 16 residues processed: 172 average time/residue: 0.2777 time to fit residues: 63.7940 Evaluate side-chains 176 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 451 ARG Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 1053 CYS Chi-restraints excluded: chain A residue 1310 PHE Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1692 THR Chi-restraints excluded: chain A residue 1747 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 27 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 chunk 85 optimal weight: 0.0970 chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 121 optimal weight: 7.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.194619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.163814 restraints weight = 52795.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.169789 restraints weight = 23766.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.173442 restraints weight = 13434.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.175263 restraints weight = 9107.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.176982 restraints weight = 7281.938| |-----------------------------------------------------------------------------| r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10066 Z= 0.123 Angle : 0.524 5.347 13634 Z= 0.270 Chirality : 0.040 0.313 1552 Planarity : 0.004 0.062 1732 Dihedral : 3.973 37.188 1353 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.47 % Allowed : 13.22 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.25), residues: 1208 helix: 1.29 (0.21), residues: 606 sheet: -0.92 (0.46), residues: 140 loop : -0.46 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 821 TYR 0.011 0.001 TYR A 47 PHE 0.010 0.001 PHE A1700 TRP 0.028 0.002 TRP A 133 HIS 0.012 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (10066) covalent geometry : angle 0.52437 / 0.27 (13634) hydrogen bonds : bond 0.03790 / 2.53 ( 489) hydrogen bonds : angle 4.22152 / 3.11 ( 1398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3414.78 seconds wall clock time: 58 minutes 56.21 seconds (3536.21 seconds total)