Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 08:49:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yz4_14387/04_2023/7yz4_14387.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yz4_14387/04_2023/7yz4_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_14387/04_2023/7yz4_14387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yz4_14387/04_2023/7yz4_14387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yz4_14387/04_2023/7yz4_14387.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yz4_14387/04_2023/7yz4_14387.pdb" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 8.87, 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: 16.15 Conformation dependent library (CDL) restraints added in 1.6 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: 0.82 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: 7.79 Time building geometry restraints manager: 16.88 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: 7545 17.19 - 34.37: 430 34.37 - 51.56: 89 51.56 - 68.74: 11 68.74 - 85.93: 9 Dihedral angle restraints: 8084 sinusoidal: 3820 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 8081 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: 2.480 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: 0.320 Extract box with map and model: 12.950 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 61.630 Find NCS groups from input model: 0.360 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.110 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.477 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 outliers start: 10 outliers final: 3 residues processed: 217 average time/residue: 0.6636 time to fit residues: 187.3240 Evaluate side-chains 164 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 161 time to evaluate : 1.507 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2509 time to fit residues: 3.3831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 51 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 37 optimal weight: 0.0020 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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: 0.6327 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 10066 Z= 0.185 Angle : 0.560 5.272 13634 Z= 0.292 Chirality : 0.040 0.315 1552 Planarity : 0.004 0.043 1732 Dihedral : 3.684 19.880 1351 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 0.83 % 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 (0.24), residues: 1208 helix: 0.35 (0.20), residues: 607 sheet: -1.03 (0.49), residues: 130 loop : -1.09 (0.28), residues: 471 *********************** 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 172 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 163 time to evaluate : 1.958 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 outliers start: 9 outliers final: 5 residues processed: 168 average time/residue: 0.6707 time to fit residues: 148.5188 Evaluate side-chains 162 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 157 time to evaluate : 1.547 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2610 time to fit residues: 4.4110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 92 optimal weight: 0.1980 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 111 optimal weight: 0.4980 chunk 120 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 110 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 10066 Z= 0.169 Angle : 0.514 5.001 13634 Z= 0.264 Chirality : 0.039 0.320 1552 Planarity : 0.004 0.050 1732 Dihedral : 3.578 21.874 1351 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 0.83 % 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: 0.02 (0.24), residues: 1208 helix: 0.88 (0.21), residues: 607 sheet: -0.95 (0.47), residues: 134 loop : -0.74 (0.30), residues: 467 *********************** 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 166 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 157 time to evaluate : 1.528 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 outliers start: 9 outliers final: 5 residues processed: 161 average time/residue: 0.6626 time to fit residues: 139.4640 Evaluate side-chains 161 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 156 time to evaluate : 1.508 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2539 time to fit residues: 4.2444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 112 optimal weight: 0.2980 chunk 118 optimal weight: 30.0000 chunk 106 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A1339 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 10066 Z= 0.199 Angle : 0.514 5.021 13634 Z= 0.266 Chirality : 0.040 0.324 1552 Planarity : 0.004 0.061 1732 Dihedral : 3.614 23.320 1351 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.73 % 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: 0.22 (0.25), residues: 1208 helix: 1.07 (0.21), residues: 608 sheet: -0.87 (0.45), residues: 139 loop : -0.66 (0.30), residues: 461 *********************** 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 168 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 1.551 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 outliers start: 8 outliers final: 6 residues processed: 164 average time/residue: 0.6828 time to fit residues: 147.8303 Evaluate side-chains 164 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 1.470 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2433 time to fit residues: 4.7476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 0.0010 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 106 optimal weight: 0.0970 chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 224 GLN A 356 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 10066 Z= 0.172 Angle : 0.498 4.908 13634 Z= 0.254 Chirality : 0.039 0.319 1552 Planarity : 0.004 0.058 1732 Dihedral : 3.563 22.634 1351 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 0.73 % 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: 0.43 (0.25), residues: 1208 helix: 1.29 (0.21), residues: 609 sheet: -0.78 (0.46), residues: 140 loop : -0.64 (0.30), residues: 459 *********************** 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 fitting. rotamer outliers: 8 poor density : 162 time to evaluate : 1.473 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 outliers start: 8 outliers final: 5 residues processed: 165 average time/residue: 0.6833 time to fit residues: 147.0158 Evaluate side-chains 161 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 156 time to evaluate : 1.735 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2858 time to fit residues: 4.9468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 69 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 119 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 114 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 10066 Z= 0.188 Angle : 0.503 5.740 13634 Z= 0.257 Chirality : 0.039 0.325 1552 Planarity : 0.004 0.059 1732 Dihedral : 3.583 22.897 1351 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.64 % 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: 1.35 (0.21), residues: 610 sheet: -0.75 (0.46), residues: 140 loop : -0.61 (0.30), residues: 458 *********************** 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 167 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 160 time to evaluate : 1.577 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 outliers start: 7 outliers final: 5 residues processed: 164 average time/residue: 0.6798 time to fit residues: 145.9319 Evaluate side-chains 159 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 154 time to evaluate : 1.497 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4317 time to fit residues: 5.1829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 118 optimal weight: 50.0000 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 10066 Z= 0.318 Angle : 0.573 5.320 13634 Z= 0.307 Chirality : 0.041 0.336 1552 Planarity : 0.005 0.058 1732 Dihedral : 3.979 26.525 1351 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer Outliers : 0.92 % 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: 0.20 (0.25), residues: 1208 helix: 1.02 (0.21), residues: 605 sheet: -0.73 (0.48), residues: 135 loop : -0.68 (0.30), residues: 468 *********************** 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 168 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 1.570 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 outliers start: 10 outliers final: 9 residues processed: 163 average time/residue: 0.6955 time to fit residues: 148.4926 Evaluate side-chains 161 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 1.416 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2418 time to fit residues: 5.8229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 0.0970 chunk 107 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.6452 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 10066 Z= 0.241 Angle : 0.538 5.837 13634 Z= 0.282 Chirality : 0.040 0.322 1552 Planarity : 0.004 0.060 1732 Dihedral : 3.911 25.065 1351 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 0.28 % 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: 0.28 (0.25), residues: 1208 helix: 1.06 (0.21), residues: 613 sheet: -0.68 (0.48), residues: 135 loop : -0.63 (0.30), residues: 460 *********************** 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 157 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 154 time to evaluate : 1.571 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 outliers start: 3 outliers final: 2 residues processed: 155 average time/residue: 0.7186 time to fit residues: 144.2565 Evaluate side-chains 150 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 148 time to evaluate : 1.372 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2794 time to fit residues: 2.9484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 113 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 10066 Z= 0.274 Angle : 0.551 6.010 13634 Z= 0.291 Chirality : 0.041 0.327 1552 Planarity : 0.004 0.059 1732 Dihedral : 3.972 25.433 1351 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.64 % 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: 0.23 (0.25), residues: 1208 helix: 1.00 (0.21), residues: 613 sheet: -0.68 (0.47), residues: 135 loop : -0.64 (0.30), residues: 460 *********************** 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 156 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 149 time to evaluate : 1.501 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 outliers start: 7 outliers final: 5 residues processed: 150 average time/residue: 0.6872 time to fit residues: 133.7913 Evaluate side-chains 152 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 147 time to evaluate : 1.466 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4368 time to fit residues: 5.2399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 122 optimal weight: 40.0000 chunk 112 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- 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: 0.6474 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 10066 Z= 0.255 Angle : 0.550 7.137 13634 Z= 0.289 Chirality : 0.041 0.324 1552 Planarity : 0.004 0.060 1732 Dihedral : 3.981 25.149 1351 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 0.09 % 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: 0.21 (0.25), residues: 1208 helix: 1.01 (0.21), residues: 613 sheet: -0.87 (0.46), residues: 140 loop : -0.61 (0.30), residues: 455 ********************** 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 152 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 1.590 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 outliers start: 1 outliers final: 1 residues processed: 152 average time/residue: 0.7073 time to fit residues: 140.9850 Evaluate side-chains 153 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 1.615 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2329 time to fit residues: 2.6571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.3980 chunk 89 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 40 optimal weight: 0.0010 chunk 100 optimal weight: 0.3980 chunk 12 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 overall best weight: 0.2186 ------------------------------------------------------------------------------- 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 356 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.203360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.173053 restraints weight = 53219.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.179182 restraints weight = 23394.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.182929 restraints weight = 13138.363| |-----------------------------------------------------------------------------| r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.055 10066 Z= 0.149 Angle : 0.515 5.495 13634 Z= 0.260 Chirality : 0.039 0.310 1552 Planarity : 0.004 0.060 1732 Dihedral : 3.737 21.901 1351 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.28 % 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: 1.37 (0.21), residues: 614 sheet: -0.67 (0.48), residues: 126 loop : -0.50 (0.30), residues: 468 =============================================================================== Job complete usr+sys time: 4706.79 seconds wall clock time: 83 minutes 57.86 seconds (5037.86 seconds total)