Starting phenix.real_space_refine on Mon Mar 18 02:54:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yz4_14387/03_2024/7yz4_14387.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yz4_14387/03_2024/7yz4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yz4_14387/03_2024/7yz4_14387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yz4_14387/03_2024/7yz4_14387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yz4_14387/03_2024/7yz4_14387.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yz4_14387/03_2024/7yz4_14387.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 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: 8.85, per 1000 atoms: 0.45 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.90 Conformation dependent library (CDL) restraints added in 1.9 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: 1.79 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: 7.16 Time building geometry restraints manager: 15.54 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: 72.31 - 84.68: 3 84.68 - 97.05: 0 97.05 - 109.42: 13447 109.42 - 121.79: 19380 121.79 - 134.16: 3468 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 1.850 nonbonded pdb=" HG1 THR A1867 " pdb=" OD1 ASP A1869 " model vdw 1.669 1.850 nonbonded pdb=" O GLU A 542 " pdb=" HG SER A 545 " model vdw 1.683 1.850 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 1.850 ... (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: 3.780 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: 12.410 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 60.920 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.990 ------------------------------------------------------------------------------- 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= 0.282 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 *********************** 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 fitting. rotamer outliers: 10 poor density : 210 time to evaluate : 1.402 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: 0.6533 time to fit residues: 184.2003 Evaluate side-chains 167 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 164 time to evaluate : 1.424 ------------------------------------------------------------------------------- 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: 6.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 96 optimal weight: 0.1980 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10066 Z= 0.206 Angle : 0.560 5.250 13634 Z= 0.295 Chirality : 0.040 0.321 1552 Planarity : 0.004 0.045 1732 Dihedral : 3.902 33.300 1355 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.92 % Allowed : 10.10 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.67 (0.24), residues: 1208 helix: 0.30 (0.20), residues: 609 sheet: -1.07 (0.48), residues: 131 loop : -1.13 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 316 HIS 0.007 0.001 HIS A 356 PHE 0.020 0.001 PHE A1700 TYR 0.018 0.001 TYR A1335 ARG 0.006 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue THR 655 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue ILE 907 is missing expected H atoms. Skipping. Residue ILE 909 is missing expected H atoms. Skipping. Residue SER 911 is missing expected H atoms. Skipping. Residue THR 912 is missing expected H atoms. Skipping. Residue LYS 913 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue SER 915 is missing expected H atoms. Skipping. Residue LYS 916 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 166 time to evaluate : 1.517 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 222 LYS cc_start: 0.7651 (mmtt) cc_final: 0.7421 (ttpt) REVERT: A 307 ARG cc_start: 0.8197 (ptp-110) cc_final: 0.7910 (ptp-110) REVERT: A 325 MET cc_start: 0.7661 (mtt) cc_final: 0.7354 (mtt) REVERT: A 477 ASN cc_start: 0.7951 (t0) cc_final: 0.7268 (m-40) REVERT: A 546 TYR cc_start: 0.8157 (t80) cc_final: 0.7711 (t80) REVERT: A 771 TYR cc_start: 0.6996 (m-80) cc_final: 0.6260 (m-80) REVERT: A 791 LYS cc_start: 0.8388 (pttt) cc_final: 0.7997 (ptmm) REVERT: A 851 GLN cc_start: 0.7202 (pt0) cc_final: 0.6864 (pt0) REVERT: A 1066 THR cc_start: 0.7722 (m) cc_final: 0.7444 (p) REVERT: A 1345 TYR cc_start: 0.7030 (t80) cc_final: 0.6733 (t80) REVERT: A 1746 TYR cc_start: 0.7676 (m-80) cc_final: 0.7393 (m-80) REVERT: A 1768 LYS cc_start: 0.7068 (mttt) cc_final: 0.6734 (mmmt) REVERT: A 1815 MET cc_start: 0.7696 (tpt) cc_final: 0.7363 (tpt) outliers start: 10 outliers final: 6 residues processed: 172 average time/residue: 0.6352 time to fit residues: 142.3919 Evaluate side-chains 163 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 157 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER 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 Chi-restraints excluded: chain A residue 1682 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 chunk 99 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 38 optimal weight: 0.1980 chunk 89 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1339 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10066 Z= 0.193 Angle : 0.517 5.084 13634 Z= 0.270 Chirality : 0.039 0.323 1552 Planarity : 0.004 0.048 1732 Dihedral : 3.820 35.269 1354 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.65 % Allowed : 10.47 % 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: -0.07 (0.24), residues: 1208 helix: 0.81 (0.21), residues: 607 sheet: -0.96 (0.47), residues: 135 loop : -0.80 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 316 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 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue THR 655 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue ILE 907 is missing expected H atoms. Skipping. Residue ILE 909 is missing expected H atoms. Skipping. Residue SER 911 is missing expected H atoms. Skipping. Residue THR 912 is missing expected H atoms. Skipping. Residue LYS 913 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue SER 915 is missing expected H atoms. Skipping. Residue LYS 916 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 1.527 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: A 325 MET cc_start: 0.7656 (mtt) cc_final: 0.7333 (mtt) REVERT: A 477 ASN cc_start: 0.8115 (t0) cc_final: 0.7256 (m-40) REVERT: A 546 TYR cc_start: 0.7948 (t80) cc_final: 0.7644 (t80) REVERT: A 791 LYS cc_start: 0.8454 (pttt) cc_final: 0.8094 (ptmm) REVERT: A 1066 THR cc_start: 0.7680 (m) cc_final: 0.7373 (p) REVERT: A 1345 TYR cc_start: 0.7072 (t80) cc_final: 0.6768 (t80) REVERT: A 1661 GLU cc_start: 0.5449 (pm20) cc_final: 0.4805 (pm20) REVERT: A 1768 LYS cc_start: 0.7129 (mttt) cc_final: 0.6780 (mmmt) REVERT: A 1815 MET cc_start: 0.7749 (tpt) cc_final: 0.7405 (tpt) outliers start: 18 outliers final: 14 residues processed: 170 average time/residue: 0.6508 time to fit residues: 145.3081 Evaluate side-chains 170 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 152 CYS 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 566 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 118 optimal weight: 40.0000 chunk 106 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10066 Z= 0.240 Angle : 0.532 5.132 13634 Z= 0.280 Chirality : 0.040 0.327 1552 Planarity : 0.004 0.063 1732 Dihedral : 3.942 36.609 1354 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.84 % Allowed : 10.28 % 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: 0.14 (0.25), residues: 1208 helix: 1.01 (0.21), residues: 602 sheet: -0.79 (0.47), residues: 136 loop : -0.76 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 133 HIS 0.005 0.001 HIS A1713 PHE 0.016 0.001 PHE A1700 TYR 0.010 0.001 TYR A 546 ARG 0.003 0.000 ARG A 269 *********************** 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 182 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 1.484 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 325 MET cc_start: 0.7690 (mtt) cc_final: 0.7449 (mtt) REVERT: A 546 TYR cc_start: 0.7974 (t80) cc_final: 0.7684 (t80) REVERT: A 791 LYS cc_start: 0.8471 (pttt) cc_final: 0.8126 (ptmm) REVERT: A 1066 THR cc_start: 0.7635 (m) cc_final: 0.7304 (p) REVERT: A 1345 TYR cc_start: 0.7121 (t80) cc_final: 0.6760 (t80) REVERT: A 1661 GLU cc_start: 0.4753 (pm20) cc_final: 0.3948 (pm20) REVERT: A 1768 LYS cc_start: 0.7175 (mttt) cc_final: 0.6798 (mmmt) outliers start: 20 outliers final: 16 residues processed: 176 average time/residue: 0.6549 time to fit residues: 150.8449 Evaluate side-chains 171 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 152 CYS 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 994 SER 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 67 optimal weight: 0.0770 chunk 1 optimal weight: 0.0050 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.0670 chunk 101 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 60 optimal weight: 0.0030 chunk 106 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.0498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 10066 Z= 0.140 Angle : 0.486 4.744 13634 Z= 0.244 Chirality : 0.039 0.308 1552 Planarity : 0.004 0.063 1732 Dihedral : 3.686 36.561 1354 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.47 % Allowed : 11.48 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.25), residues: 1208 helix: 1.38 (0.21), residues: 610 sheet: -0.71 (0.46), residues: 141 loop : -0.56 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 133 HIS 0.005 0.001 HIS A1761 PHE 0.010 0.001 PHE A 896 TYR 0.010 0.001 TYR A 546 ARG 0.007 0.000 ARG A1719 *********************** 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 174 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 158 time to evaluate : 1.326 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: A 133 TRP cc_start: 0.7446 (m100) cc_final: 0.7222 (m100) REVERT: A 324 MET cc_start: 0.6884 (mpp) cc_final: 0.6332 (tpp) REVERT: A 325 MET cc_start: 0.7591 (mtt) cc_final: 0.7224 (mtt) REVERT: A 546 TYR cc_start: 0.7846 (t80) cc_final: 0.7529 (t80) REVERT: A 791 LYS cc_start: 0.8444 (pttt) cc_final: 0.8109 (ptmm) REVERT: A 1066 THR cc_start: 0.7600 (m) cc_final: 0.7289 (p) REVERT: A 1345 TYR cc_start: 0.7063 (t80) cc_final: 0.6739 (t80) REVERT: A 1553 LYS cc_start: 0.7572 (tptt) cc_final: 0.7285 (tptt) REVERT: A 1661 GLU cc_start: 0.4750 (pm20) cc_final: 0.3933 (pm20) REVERT: A 1768 LYS cc_start: 0.7061 (mttt) cc_final: 0.6703 (mmmt) outliers start: 16 outliers final: 10 residues processed: 168 average time/residue: 0.6439 time to fit residues: 141.0330 Evaluate side-chains 164 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 154 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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 362 TYR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 566 THR 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 1808 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 chunk 119 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10066 Z= 0.220 Angle : 0.512 5.772 13634 Z= 0.266 Chirality : 0.039 0.327 1552 Planarity : 0.004 0.061 1732 Dihedral : 3.768 36.808 1354 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.74 % Allowed : 11.02 % Favored : 87.24 % 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: 0.61 (0.25), residues: 1208 helix: 1.39 (0.21), residues: 610 sheet: -0.62 (0.47), residues: 139 loop : -0.53 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 316 HIS 0.012 0.001 HIS A 178 PHE 0.016 0.001 PHE A 896 TYR 0.010 0.001 TYR A1695 ARG 0.004 0.000 ARG A 95 *********************** 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 171 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 1.430 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 324 MET cc_start: 0.6963 (mpp) cc_final: 0.6403 (tpp) REVERT: A 325 MET cc_start: 0.7721 (mtt) cc_final: 0.7405 (mtt) REVERT: A 546 TYR cc_start: 0.7915 (t80) cc_final: 0.7554 (t80) REVERT: A 791 LYS cc_start: 0.8473 (pttt) cc_final: 0.8037 (pptt) REVERT: A 1066 THR cc_start: 0.7625 (m) cc_final: 0.7375 (p) REVERT: A 1345 TYR cc_start: 0.7107 (t80) cc_final: 0.6760 (t80) REVERT: A 1661 GLU cc_start: 0.4306 (pm20) cc_final: 0.3392 (pm20) REVERT: A 1768 LYS cc_start: 0.7148 (mttt) cc_final: 0.6778 (mmmt) outliers start: 19 outliers final: 15 residues processed: 165 average time/residue: 0.6554 time to fit residues: 141.6638 Evaluate side-chains 163 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 152 CYS 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 480 THR Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1310 PHE Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1577 LEU Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1692 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1683 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 10066 Z= 0.412 Angle : 0.627 5.732 13634 Z= 0.344 Chirality : 0.043 0.339 1552 Planarity : 0.005 0.063 1732 Dihedral : 4.347 37.647 1353 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.48 % Allowed : 11.29 % Favored : 86.23 % 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: -0.07 (0.24), residues: 1208 helix: 0.71 (0.21), residues: 606 sheet: -0.70 (0.49), residues: 133 loop : -0.74 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 316 HIS 0.014 0.002 HIS A 178 PHE 0.021 0.002 PHE A1681 TYR 0.017 0.002 TYR A 927 ARG 0.009 0.001 ARG A1719 *********************** 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 189 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8645 (tttt) cc_final: 0.8161 (tttt) REVERT: A 304 SER cc_start: 0.8898 (t) cc_final: 0.8672 (p) REVERT: A 537 PHE cc_start: 0.7740 (m-80) cc_final: 0.7474 (m-80) REVERT: A 546 TYR cc_start: 0.8046 (t80) cc_final: 0.7592 (t80) REVERT: A 746 ARG cc_start: 0.6556 (ppt170) cc_final: 0.5886 (ppt170) REVERT: A 791 LYS cc_start: 0.8624 (pttt) cc_final: 0.8316 (ptmm) REVERT: A 851 GLN cc_start: 0.7287 (pt0) cc_final: 0.6946 (pt0) REVERT: A 1066 THR cc_start: 0.7616 (m) cc_final: 0.7374 (p) REVERT: A 1345 TYR cc_start: 0.7210 (t80) cc_final: 0.6790 (t80) REVERT: A 1547 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6939 (mt-10) REVERT: A 1661 GLU cc_start: 0.4576 (pm20) cc_final: 0.4155 (pm20) REVERT: A 1758 GLU cc_start: 0.7492 (tt0) cc_final: 0.7234 (tt0) REVERT: A 1768 LYS cc_start: 0.7389 (mttt) cc_final: 0.7151 (tppt) REVERT: A 1769 PHE cc_start: 0.6452 (t80) cc_final: 0.6194 (t80) REVERT: A 1815 MET cc_start: 0.7801 (tpt) cc_final: 0.7515 (tpt) outliers start: 27 outliers final: 24 residues processed: 180 average time/residue: 0.6526 time to fit residues: 154.1717 Evaluate side-chains 181 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 157 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1310 PHE Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1692 THR Chi-restraints excluded: chain A residue 1808 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 4.9990 chunk 35 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 0.0770 chunk 107 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10066 Z= 0.188 Angle : 0.521 5.795 13634 Z= 0.270 Chirality : 0.040 0.313 1552 Planarity : 0.004 0.065 1732 Dihedral : 4.016 36.478 1353 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.74 % Allowed : 12.67 % Favored : 85.58 % 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: 0.31 (0.25), residues: 1208 helix: 1.11 (0.21), residues: 604 sheet: -0.71 (0.48), residues: 132 loop : -0.60 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 316 HIS 0.014 0.001 HIS A 178 PHE 0.019 0.001 PHE A 896 TYR 0.013 0.001 TYR A 543 ARG 0.005 0.000 ARG A 95 *********************** 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 fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 SER cc_start: 0.8796 (t) cc_final: 0.8570 (p) REVERT: A 466 LYS cc_start: 0.7457 (mttp) cc_final: 0.7214 (mmtm) REVERT: A 537 PHE cc_start: 0.7691 (m-80) cc_final: 0.7464 (m-80) REVERT: A 546 TYR cc_start: 0.7928 (t80) cc_final: 0.7541 (t80) REVERT: A 746 ARG cc_start: 0.6646 (ppt170) cc_final: 0.5838 (ppt170) REVERT: A 791 LYS cc_start: 0.8615 (pttt) cc_final: 0.8312 (ptmm) REVERT: A 1066 THR cc_start: 0.7597 (m) cc_final: 0.7358 (p) REVERT: A 1345 TYR cc_start: 0.7190 (t80) cc_final: 0.6772 (t80) REVERT: A 1547 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6720 (mt-10) REVERT: A 1661 GLU cc_start: 0.4437 (pm20) cc_final: 0.4032 (pm20) REVERT: A 1758 GLU cc_start: 0.7238 (tt0) cc_final: 0.7033 (tt0) REVERT: A 1768 LYS cc_start: 0.7220 (mttt) cc_final: 0.6854 (mmmt) outliers start: 19 outliers final: 15 residues processed: 171 average time/residue: 0.6920 time to fit residues: 153.7199 Evaluate side-chains 171 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 451 ARG Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 994 SER 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 1808 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10066 Z= 0.224 Angle : 0.522 5.053 13634 Z= 0.273 Chirality : 0.040 0.321 1552 Planarity : 0.004 0.063 1732 Dihedral : 3.958 36.634 1353 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.74 % Allowed : 12.76 % 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: 0.42 (0.25), residues: 1208 helix: 1.23 (0.21), residues: 604 sheet: -0.76 (0.48), residues: 132 loop : -0.56 (0.30), residues: 472 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 0.011 0.001 TYR A 543 ARG 0.005 0.000 ARG A 95 *********************** 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 175 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 156 time to evaluate : 1.346 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 304 SER cc_start: 0.8823 (t) cc_final: 0.8599 (p) REVERT: A 546 TYR cc_start: 0.7934 (t80) cc_final: 0.7595 (t80) REVERT: A 746 ARG cc_start: 0.6721 (ppt170) cc_final: 0.5890 (ppt170) REVERT: A 791 LYS cc_start: 0.8627 (pttt) cc_final: 0.8324 (ptmm) REVERT: A 1066 THR cc_start: 0.7605 (m) cc_final: 0.7370 (p) REVERT: A 1345 TYR cc_start: 0.7186 (t80) cc_final: 0.6757 (t80) REVERT: A 1547 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6729 (mt-10) REVERT: A 1661 GLU cc_start: 0.4410 (pm20) cc_final: 0.4027 (pm20) REVERT: A 1758 GLU cc_start: 0.7302 (tt0) cc_final: 0.7081 (tt0) REVERT: A 1768 LYS cc_start: 0.7213 (mttt) cc_final: 0.6853 (mmmt) REVERT: A 1815 MET cc_start: 0.7709 (tpt) cc_final: 0.7433 (tpt) outliers start: 19 outliers final: 18 residues processed: 169 average time/residue: 0.6712 time to fit residues: 147.7358 Evaluate side-chains 172 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 451 ARG Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1053 CYS Chi-restraints excluded: chain A residue 1310 PHE Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1808 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 40.0000 chunk 112 optimal weight: 0.0060 chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10066 Z= 0.198 Angle : 0.513 5.643 13634 Z= 0.267 Chirality : 0.039 0.319 1552 Planarity : 0.004 0.064 1732 Dihedral : 3.895 36.679 1353 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.65 % Allowed : 13.13 % Favored : 85.22 % 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: 0.50 (0.25), residues: 1208 helix: 1.29 (0.21), residues: 611 sheet: -0.72 (0.50), residues: 118 loop : -0.56 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 316 HIS 0.011 0.001 HIS A 178 PHE 0.018 0.001 PHE A 896 TYR 0.010 0.001 TYR A 927 ARG 0.004 0.000 ARG A 95 ********************** 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 173 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 1.344 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: A 304 SER cc_start: 0.8818 (t) cc_final: 0.8593 (p) REVERT: A 466 LYS cc_start: 0.7457 (mttp) cc_final: 0.7196 (mmtm) REVERT: A 537 PHE cc_start: 0.7720 (m-80) cc_final: 0.7301 (m-10) REVERT: A 546 TYR cc_start: 0.7913 (t80) cc_final: 0.7508 (t80) REVERT: A 746 ARG cc_start: 0.6727 (ppt170) cc_final: 0.6035 (ppt170) REVERT: A 791 LYS cc_start: 0.8619 (pttt) cc_final: 0.8310 (ptmm) REVERT: A 1066 THR cc_start: 0.7604 (m) cc_final: 0.7379 (p) REVERT: A 1345 TYR cc_start: 0.7214 (t80) cc_final: 0.6841 (t80) REVERT: A 1547 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6739 (mt-10) REVERT: A 1661 GLU cc_start: 0.4396 (pm20) cc_final: 0.4071 (pm20) REVERT: A 1768 LYS cc_start: 0.7189 (mttt) cc_final: 0.6958 (tppt) outliers start: 18 outliers final: 18 residues processed: 168 average time/residue: 0.6452 time to fit residues: 140.7757 Evaluate side-chains 173 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 451 ARG Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1053 CYS Chi-restraints excluded: chain A residue 1310 PHE Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1577 LEU Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1808 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.0570 chunk 89 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 100 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 5 optimal weight: 0.0980 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.196184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.167667 restraints weight = 52784.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.173448 restraints weight = 24886.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.174633 restraints weight = 12717.258| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 10066 Z= 0.154 Angle : 0.498 5.696 13634 Z= 0.254 Chirality : 0.039 0.314 1552 Planarity : 0.004 0.063 1732 Dihedral : 3.732 36.054 1353 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.38 % Allowed : 13.77 % Favored : 84.85 % 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 (0.25), residues: 1208 helix: 1.48 (0.21), residues: 611 sheet: -0.68 (0.50), residues: 120 loop : -0.47 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 316 HIS 0.010 0.001 HIS A 178 PHE 0.019 0.001 PHE A 896 TYR 0.009 0.001 TYR A 546 ARG 0.004 0.000 ARG A 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4733.56 seconds wall clock time: 84 minutes 6.66 seconds (5046.66 seconds total)