Starting phenix.real_space_refine on Tue Jun 17 15:50:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yz4_14387/06_2025/7yz4_14387.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yz4_14387/06_2025/7yz4_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yz4_14387/06_2025/7yz4_14387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yz4_14387/06_2025/7yz4_14387.map" model { file = "/net/cci-nas-00/data/ceres_data/7yz4_14387/06_2025/7yz4_14387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yz4_14387/06_2025/7yz4_14387.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 11.74, per 1000 atoms: 0.59 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: 4.96 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.69 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: 8.40 Time building geometry restraints manager: 6.06 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: 8.040 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: 0.310 Extract box with map and model: 1.050 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 45.960 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6269 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.027 0.005 TRP A 133 HIS 0.013 0.002 HIS A 58 PHE 0.030 0.003 PHE A1700 TYR 0.032 0.003 TYR A1695 ARG 0.032 0.003 ARG A 790 Details of bonding type rmsd hydrogen bonds : bond 0.15257 ( 489) hydrogen bonds : angle 6.07495 ( 1398) covalent geometry : bond 0.00432 (10066) covalent geometry : angle 0.78015 (13634) *********************** 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 : 1.692 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 53 GLU cc_start: 0.6978 (tp30) cc_final: 0.6617 (tt0) REVERT: A 144 LYS cc_start: 0.8235 (mttt) cc_final: 0.7967 (mttp) REVERT: A 193 CYS cc_start: 0.7425 (t) cc_final: 0.7102 (t) REVERT: A 219 LEU cc_start: 0.8013 (tp) cc_final: 0.7782 (tp) REVERT: A 222 LYS cc_start: 0.7640 (mmtt) cc_final: 0.7424 (ttpt) REVERT: A 225 LYS cc_start: 0.8156 (tttp) cc_final: 0.7951 (tttt) REVERT: A 307 ARG cc_start: 0.7995 (ptp-110) cc_final: 0.7679 (ptp-110) REVERT: A 324 MET cc_start: 0.6766 (mpp) cc_final: 0.6318 (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: 0.7233 (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: 0.8132 (p) REVERT: A 771 TYR cc_start: 0.6920 (m-80) cc_final: 0.6389 (m-80) REVERT: A 791 LYS cc_start: 0.8418 (pttt) cc_final: 0.7967 (ptmm) REVERT: A 851 GLN cc_start: 0.7235 (pt0) cc_final: 0.6848 (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: 0.6709 (t80) REVERT: A 1768 LYS cc_start: 0.7039 (mttt) cc_final: 0.6710 (mmmt) outliers start: 10 outliers final: 3 residues processed: 217 average time/residue: 0.6934 time to fit residues: 196.0396 Evaluate side-chains 167 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 164 time to evaluate : 1.645 ------------------------------------------------------------------------------- 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 103 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 96 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4469 r_free = 0.4469 target = 0.198302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.167171 restraints weight = 52515.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.173214 restraints weight = 23039.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.176793 restraints weight = 12989.035| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10066 Z= 0.155 Angle : 0.572 5.271 13634 Z= 0.303 Chirality : 0.041 0.321 1552 Planarity : 0.004 0.049 1732 Dihedral : 3.956 34.245 1355 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.83 % Allowed : 10.28 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.23), residues: 1208 helix: 0.35 (0.20), residues: 603 sheet: -1.19 (0.48), residues: 133 loop : -1.23 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 316 HIS 0.007 0.001 HIS A 178 PHE 0.021 0.001 PHE A1700 TYR 0.019 0.001 TYR A1335 ARG 0.006 0.000 ARG A 137 Details of bonding type rmsd hydrogen bonds : bond 0.04912 ( 489) hydrogen bonds : angle 4.79649 ( 1398) covalent geometry : bond 0.00335 (10066) covalent geometry : angle 0.57247 (13634) *********************** 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 173 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 1.579 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 307 ARG cc_start: 0.8059 (ptp-110) cc_final: 0.7788 (ptp-110) REVERT: A 325 MET cc_start: 0.7302 (mtt) cc_final: 0.7086 (mtt) REVERT: A 477 ASN cc_start: 0.7933 (t0) cc_final: 0.7411 (m-40) REVERT: A 546 TYR cc_start: 0.8001 (t80) cc_final: 0.7566 (t80) REVERT: A 771 TYR cc_start: 0.7249 (m-80) cc_final: 0.6562 (m-80) REVERT: A 791 LYS cc_start: 0.8403 (pttt) cc_final: 0.8088 (ptmm) REVERT: A 851 GLN cc_start: 0.7327 (pt0) cc_final: 0.7047 (pt0) REVERT: A 1066 THR cc_start: 0.7786 (m) cc_final: 0.7533 (p) REVERT: A 1345 TYR cc_start: 0.7042 (t80) cc_final: 0.6733 (t80) REVERT: A 1547 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6667 (mt-10) REVERT: A 1746 TYR cc_start: 0.7643 (m-80) cc_final: 0.7422 (m-80) REVERT: A 1768 LYS cc_start: 0.7020 (mttt) cc_final: 0.6705 (mmmt) REVERT: A 1815 MET cc_start: 0.7722 (tpt) cc_final: 0.7388 (tpt) outliers start: 9 outliers final: 6 residues processed: 169 average time/residue: 0.6558 time to fit residues: 145.8305 Evaluate side-chains 162 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 156 time to evaluate : 1.635 ------------------------------------------------------------------------------- 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 117 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.0980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 HIS A1339 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.196918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.166448 restraints weight = 52357.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.172359 restraints weight = 23036.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.175945 restraints weight = 12893.848| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10066 Z= 0.136 Angle : 0.525 5.108 13634 Z= 0.274 Chirality : 0.040 0.320 1552 Planarity : 0.004 0.049 1732 Dihedral : 3.867 36.222 1354 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.92 % Allowed : 10.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.24), residues: 1208 helix: 0.87 (0.21), residues: 600 sheet: -1.09 (0.48), residues: 133 loop : -0.97 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 133 HIS 0.005 0.001 HIS A1683 PHE 0.015 0.001 PHE A1700 TYR 0.013 0.001 TYR A 47 ARG 0.005 0.000 ARG A 746 Details of bonding type rmsd hydrogen bonds : bond 0.04315 ( 489) hydrogen bonds : angle 4.47840 ( 1398) covalent geometry : bond 0.00298 (10066) covalent geometry : angle 0.52481 (13634) *********************** 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 168 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 1.423 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 137 ARG cc_start: 0.6391 (ptm160) cc_final: 0.5777 (ptm160) REVERT: A 325 MET cc_start: 0.7288 (mtt) cc_final: 0.7054 (mtt) REVERT: A 477 ASN cc_start: 0.8050 (t0) cc_final: 0.7441 (m-40) REVERT: A 546 TYR cc_start: 0.7777 (t80) cc_final: 0.7459 (t80) REVERT: A 791 LYS cc_start: 0.8421 (pttt) cc_final: 0.8126 (ptmm) REVERT: A 1066 THR cc_start: 0.7753 (m) cc_final: 0.7440 (p) REVERT: A 1345 TYR cc_start: 0.7073 (t80) cc_final: 0.6769 (t80) REVERT: A 1547 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6701 (mt-10) REVERT: A 1661 GLU cc_start: 0.5706 (pm20) cc_final: 0.4970 (pm20) REVERT: A 1768 LYS cc_start: 0.7069 (mttt) cc_final: 0.6737 (mmmt) REVERT: A 1815 MET cc_start: 0.7769 (tpt) cc_final: 0.7415 (tpt) outliers start: 10 outliers final: 9 residues processed: 166 average time/residue: 0.6576 time to fit residues: 142.3988 Evaluate side-chains 163 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 1.657 ------------------------------------------------------------------------------- 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 229 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 87 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 78 optimal weight: 0.0020 chunk 85 optimal weight: 0.0980 chunk 77 optimal weight: 0.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 356 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.197340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.167016 restraints weight = 52835.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.172985 restraints weight = 23421.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.176560 restraints weight = 13150.142| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10066 Z= 0.117 Angle : 0.505 5.272 13634 Z= 0.260 Chirality : 0.039 0.319 1552 Planarity : 0.004 0.062 1732 Dihedral : 3.793 35.872 1354 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1208 helix: 1.15 (0.21), residues: 601 sheet: -0.94 (0.47), residues: 135 loop : -0.82 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 133 HIS 0.004 0.001 HIS A1655 PHE 0.011 0.001 PHE A1700 TYR 0.020 0.001 TYR A1335 ARG 0.004 0.000 ARG A 746 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 489) hydrogen bonds : angle 4.31811 ( 1398) covalent geometry : bond 0.00258 (10066) covalent geometry : angle 0.50464 (13634) *********************** 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 173 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 1.614 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: A 477 ASN cc_start: 0.8096 (t0) cc_final: 0.7502 (m-40) REVERT: A 546 TYR cc_start: 0.7786 (t80) cc_final: 0.7450 (t80) REVERT: A 578 THR cc_start: 0.8449 (m) cc_final: 0.8242 (p) REVERT: A 791 LYS cc_start: 0.8406 (pttt) cc_final: 0.8105 (ptmm) REVERT: A 1066 THR cc_start: 0.7753 (m) cc_final: 0.7430 (p) REVERT: A 1345 TYR cc_start: 0.7070 (t80) cc_final: 0.6760 (t80) REVERT: A 1661 GLU cc_start: 0.4913 (pm20) cc_final: 0.4056 (pm20) REVERT: A 1747 ASP cc_start: 0.7254 (m-30) cc_final: 0.6956 (m-30) REVERT: A 1768 LYS cc_start: 0.7044 (mttt) cc_final: 0.6688 (mmmt) outliers start: 12 outliers final: 10 residues processed: 171 average time/residue: 0.8083 time to fit residues: 184.0199 Evaluate side-chains 164 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 3.054 ------------------------------------------------------------------------------- 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 117 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 96 optimal weight: 0.9990 chunk 99 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.196943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.166163 restraints weight = 52898.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.172184 restraints weight = 23403.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.175873 restraints weight = 13223.730| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10066 Z= 0.123 Angle : 0.512 5.273 13634 Z= 0.263 Chirality : 0.039 0.323 1552 Planarity : 0.004 0.062 1732 Dihedral : 3.791 36.118 1354 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.19 % Allowed : 11.94 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1208 helix: 1.30 (0.21), residues: 602 sheet: -0.89 (0.45), residues: 141 loop : -0.72 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 133 HIS 0.008 0.001 HIS A 178 PHE 0.012 0.001 PHE A 896 TYR 0.010 0.001 TYR A 546 ARG 0.004 0.000 ARG A 746 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 489) hydrogen bonds : angle 4.24611 ( 1398) covalent geometry : bond 0.00274 (10066) covalent geometry : angle 0.51173 (13634) *********************** 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 170 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 3.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8101 (mm) cc_final: 0.7901 (mm) REVERT: A 477 ASN cc_start: 0.8191 (t0) cc_final: 0.7571 (m-40) REVERT: A 546 TYR cc_start: 0.7783 (t80) cc_final: 0.7441 (t80) REVERT: A 684 MET cc_start: 0.5959 (mmt) cc_final: 0.5739 (mmp) REVERT: A 1066 THR cc_start: 0.7729 (m) cc_final: 0.7385 (p) REVERT: A 1345 TYR cc_start: 0.7070 (t80) cc_final: 0.6758 (t80) REVERT: A 1661 GLU cc_start: 0.4707 (pm20) cc_final: 0.3902 (pm20) REVERT: A 1768 LYS cc_start: 0.7057 (mttt) cc_final: 0.6705 (mmmt) outliers start: 13 outliers final: 11 residues processed: 165 average time/residue: 0.7369 time to fit residues: 161.2021 Evaluate side-chains 164 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 1.494 ------------------------------------------------------------------------------- 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 229 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 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 71 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.196166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.164662 restraints weight = 52954.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.170558 restraints weight = 23845.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.174372 restraints weight = 13558.774| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10066 Z= 0.141 Angle : 0.514 5.054 13634 Z= 0.267 Chirality : 0.040 0.324 1552 Planarity : 0.004 0.061 1732 Dihedral : 3.841 36.745 1354 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.93 % Allowed : 11.57 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1208 helix: 1.36 (0.21), residues: 604 sheet: -0.79 (0.46), residues: 141 loop : -0.62 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 133 HIS 0.011 0.001 HIS A 178 PHE 0.018 0.001 PHE A 896 TYR 0.012 0.001 TYR A 47 ARG 0.011 0.000 ARG A1719 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 489) hydrogen bonds : angle 4.23706 ( 1398) covalent geometry : bond 0.00312 (10066) covalent geometry : angle 0.51402 (13634) *********************** 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 177 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 2.306 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 304 SER cc_start: 0.8763 (t) cc_final: 0.8539 (p) REVERT: A 477 ASN cc_start: 0.8298 (t0) cc_final: 0.7706 (m-40) REVERT: A 546 TYR cc_start: 0.7744 (t80) cc_final: 0.7388 (t80) REVERT: A 1066 THR cc_start: 0.7702 (m) cc_final: 0.7442 (p) REVERT: A 1345 TYR cc_start: 0.7133 (t80) cc_final: 0.6774 (t80) REVERT: A 1661 GLU cc_start: 0.4311 (pm20) cc_final: 0.3357 (pm20) REVERT: A 1768 LYS cc_start: 0.7084 (mttt) cc_final: 0.6718 (mmmt) outliers start: 21 outliers final: 13 residues processed: 169 average time/residue: 0.8393 time to fit residues: 190.4867 Evaluate side-chains 162 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 451 ARG Chi-restraints excluded: chain A residue 703 HIS 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 16 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 92 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.195655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.164367 restraints weight = 52538.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.170349 restraints weight = 23613.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.174021 restraints weight = 13402.592| |-----------------------------------------------------------------------------| r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10066 Z= 0.142 Angle : 0.517 4.954 13634 Z= 0.269 Chirality : 0.040 0.322 1552 Planarity : 0.004 0.061 1732 Dihedral : 3.804 37.227 1353 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.74 % Allowed : 11.94 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1208 helix: 1.38 (0.21), residues: 604 sheet: -0.82 (0.45), residues: 147 loop : -0.54 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 133 HIS 0.012 0.001 HIS A 178 PHE 0.018 0.001 PHE A 896 TYR 0.015 0.001 TYR A 927 ARG 0.003 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 489) hydrogen bonds : angle 4.19124 ( 1398) covalent geometry : bond 0.00317 (10066) covalent geometry : angle 0.51717 (13634) *********************** 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 175 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 1.773 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 304 SER cc_start: 0.8802 (t) cc_final: 0.8595 (p) REVERT: A 477 ASN cc_start: 0.8404 (t0) cc_final: 0.7783 (m-40) REVERT: A 543 TYR cc_start: 0.7433 (t80) cc_final: 0.7157 (t80) REVERT: A 546 TYR cc_start: 0.7768 (t80) cc_final: 0.7335 (t80) REVERT: A 577 LYS cc_start: 0.8730 (mtpt) cc_final: 0.8403 (ptpp) REVERT: A 746 ARG cc_start: 0.6737 (ppt170) cc_final: 0.6182 (ppt170) REVERT: A 1066 THR cc_start: 0.7666 (m) cc_final: 0.7407 (p) REVERT: A 1345 TYR cc_start: 0.7146 (t80) cc_final: 0.6786 (t80) REVERT: A 1661 GLU cc_start: 0.4348 (pm20) cc_final: 0.3476 (pm20) REVERT: A 1768 LYS cc_start: 0.7121 (mttt) cc_final: 0.6747 (mmmt) outliers start: 19 outliers final: 17 residues processed: 167 average time/residue: 0.9179 time to fit residues: 205.7595 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 : 1.904 ------------------------------------------------------------------------------- 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 229 ILE Chi-restraints excluded: chain A residue 269 ARG 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 103 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.206902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.174060 restraints weight = 51984.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.180253 restraints weight = 23652.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.184146 restraints weight = 13726.656| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10066 Z= 0.123 Angle : 0.513 4.872 13634 Z= 0.264 Chirality : 0.039 0.319 1552 Planarity : 0.004 0.062 1732 Dihedral : 3.784 37.125 1353 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.93 % Allowed : 12.12 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1208 helix: 1.47 (0.21), residues: 606 sheet: -0.80 (0.46), residues: 141 loop : -0.49 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 133 HIS 0.012 0.001 HIS A 178 PHE 0.018 0.001 PHE A 896 TYR 0.012 0.001 TYR A 47 ARG 0.012 0.000 ARG A1719 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 489) hydrogen bonds : angle 4.11880 ( 1398) covalent geometry : bond 0.00278 (10066) covalent geometry : angle 0.51278 (13634) *********************** 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 177 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.616 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: 0.8816 (t) cc_final: 0.8599 (p) REVERT: A 354 LYS cc_start: 0.7204 (mtpt) cc_final: 0.6953 (mtpp) REVERT: A 359 CYS cc_start: 0.7935 (m) cc_final: 0.7162 (p) REVERT: A 477 ASN cc_start: 0.8368 (t0) cc_final: 0.7786 (m-40) REVERT: A 546 TYR cc_start: 0.7785 (t80) cc_final: 0.7361 (t80) REVERT: A 577 LYS cc_start: 0.8733 (mtpt) cc_final: 0.8407 (ptpp) REVERT: A 746 ARG cc_start: 0.6787 (ppt170) cc_final: 0.6146 (ppt170) REVERT: A 1066 THR cc_start: 0.7614 (m) cc_final: 0.7360 (p) REVERT: A 1345 TYR cc_start: 0.7162 (t80) cc_final: 0.6774 (t80) REVERT: A 1661 GLU cc_start: 0.4217 (pm20) cc_final: 0.3495 (pm20) REVERT: A 1768 LYS cc_start: 0.7079 (mttt) cc_final: 0.6715 (mmmt) outliers start: 21 outliers final: 18 residues processed: 170 average time/residue: 1.0313 time to fit residues: 245.1745 Evaluate side-chains 171 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 3.488 ------------------------------------------------------------------------------- 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 89 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 269 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 66 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 0.0970 chunk 94 optimal weight: 0.1980 chunk 68 optimal weight: 0.4980 chunk 121 optimal weight: 30.0000 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 356 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.196561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.165824 restraints weight = 52439.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.171773 restraints weight = 23586.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.175371 restraints weight = 13373.385| |-----------------------------------------------------------------------------| r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10066 Z= 0.111 Angle : 0.507 5.163 13634 Z= 0.260 Chirality : 0.039 0.318 1552 Planarity : 0.004 0.062 1732 Dihedral : 3.741 37.008 1353 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.65 % Allowed : 12.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1208 helix: 1.56 (0.21), residues: 606 sheet: -0.80 (0.46), residues: 141 loop : -0.39 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 316 HIS 0.013 0.001 HIS A 178 PHE 0.018 0.001 PHE A 896 TYR 0.012 0.001 TYR A 47 ARG 0.005 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.03559 ( 489) hydrogen bonds : angle 4.04220 ( 1398) covalent geometry : bond 0.00255 (10066) covalent geometry : angle 0.50694 (13634) *********************** 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 173 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 2.547 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: A 304 SER cc_start: 0.8783 (t) cc_final: 0.8575 (p) REVERT: A 354 LYS cc_start: 0.7255 (mtpt) cc_final: 0.6873 (mtpp) REVERT: A 359 CYS cc_start: 0.7972 (m) cc_final: 0.7163 (p) REVERT: A 466 LYS cc_start: 0.7589 (mptt) cc_final: 0.7265 (mmtm) REVERT: A 477 ASN cc_start: 0.8374 (t0) cc_final: 0.7790 (m-40) REVERT: A 537 PHE cc_start: 0.7414 (m-80) cc_final: 0.7197 (m-80) REVERT: A 546 TYR cc_start: 0.7631 (t80) cc_final: 0.7250 (t80) REVERT: A 577 LYS cc_start: 0.8662 (mtpt) cc_final: 0.8371 (ptpp) REVERT: A 746 ARG cc_start: 0.6895 (ppt170) cc_final: 0.6213 (ppt170) REVERT: A 1066 THR cc_start: 0.7668 (m) cc_final: 0.7408 (p) REVERT: A 1345 TYR cc_start: 0.7077 (t80) cc_final: 0.6712 (t80) REVERT: A 1661 GLU cc_start: 0.4239 (pm20) cc_final: 0.3632 (pm20) REVERT: A 1768 LYS cc_start: 0.7053 (mttt) cc_final: 0.6687 (mmmt) REVERT: A 1815 MET cc_start: 0.7620 (tpt) cc_final: 0.7268 (tpt) outliers start: 18 outliers final: 18 residues processed: 168 average time/residue: 1.0943 time to fit residues: 251.1389 Evaluate side-chains 169 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 2.218 ------------------------------------------------------------------------------- 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 89 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 269 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 122 optimal weight: 50.0000 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 75 optimal weight: 0.0370 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.195989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.164997 restraints weight = 52503.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.170967 restraints weight = 23790.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.174638 restraints weight = 13546.122| |-----------------------------------------------------------------------------| r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10066 Z= 0.135 Angle : 0.522 5.104 13634 Z= 0.270 Chirality : 0.040 0.324 1552 Planarity : 0.005 0.076 1732 Dihedral : 3.796 36.985 1353 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.74 % Allowed : 12.86 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1208 helix: 1.56 (0.21), residues: 606 sheet: -0.81 (0.46), residues: 141 loop : -0.38 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 133 HIS 0.012 0.001 HIS A 178 PHE 0.018 0.001 PHE A 896 TYR 0.012 0.001 TYR A 47 ARG 0.011 0.000 ARG A1719 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 489) hydrogen bonds : angle 4.12398 ( 1398) covalent geometry : bond 0.00306 (10066) covalent geometry : angle 0.52173 (13634) ********************** 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 172 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 1.626 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 304 SER cc_start: 0.8793 (t) cc_final: 0.8585 (p) REVERT: A 354 LYS cc_start: 0.7264 (mtpt) cc_final: 0.6965 (mtpp) REVERT: A 359 CYS cc_start: 0.8050 (m) cc_final: 0.7239 (p) REVERT: A 477 ASN cc_start: 0.8399 (t0) cc_final: 0.7842 (m-40) REVERT: A 546 TYR cc_start: 0.7644 (t80) cc_final: 0.7273 (t80) REVERT: A 746 ARG cc_start: 0.6980 (ppt170) cc_final: 0.6294 (ppt170) REVERT: A 1066 THR cc_start: 0.7684 (m) cc_final: 0.7418 (p) REVERT: A 1345 TYR cc_start: 0.7102 (t80) cc_final: 0.6745 (t80) REVERT: A 1661 GLU cc_start: 0.4441 (pm20) cc_final: 0.3889 (pm20) REVERT: A 1768 LYS cc_start: 0.7089 (mttt) cc_final: 0.6751 (mmmt) REVERT: A 1815 MET cc_start: 0.7639 (tpt) cc_final: 0.7285 (tpt) outliers start: 19 outliers final: 17 residues processed: 166 average time/residue: 0.6513 time to fit residues: 143.3278 Evaluate side-chains 169 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 89 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 269 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 58 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 122 optimal weight: 50.0000 chunk 1 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1683 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.197832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.167674 restraints weight = 51559.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.174422 restraints weight = 24788.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.175884 restraints weight = 11705.663| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10066 Z= 0.221 Angle : 0.579 5.416 13634 Z= 0.311 Chirality : 0.042 0.335 1552 Planarity : 0.005 0.063 1732 Dihedral : 4.096 37.413 1353 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.56 % Allowed : 13.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1208 helix: 1.21 (0.21), residues: 606 sheet: -0.89 (0.46), residues: 140 loop : -0.48 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 133 HIS 0.013 0.002 HIS A 178 PHE 0.017 0.001 PHE A 896 TYR 0.014 0.001 TYR A1695 ARG 0.009 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.04601 ( 489) hydrogen bonds : angle 4.46573 ( 1398) covalent geometry : bond 0.00485 (10066) covalent geometry : angle 0.57896 (13634) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8588.62 seconds wall clock time: 157 minutes 3.85 seconds (9423.85 seconds total)