Starting phenix.real_space_refine on Wed Mar 4 17:58:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z1h_14446/03_2026/7z1h_14446.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z1h_14446/03_2026/7z1h_14446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z1h_14446/03_2026/7z1h_14446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z1h_14446/03_2026/7z1h_14446.map" model { file = "/net/cci-nas-00/data/ceres_data/7z1h_14446/03_2026/7z1h_14446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z1h_14446/03_2026/7z1h_14446.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.039 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: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 9381 2.51 5 N 2590 2.21 5 O 2962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15032 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 15032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1848, 15032 Classifications: {'peptide': 1848} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 21, 'PCIS': 2, 'PTRANS': 48, 'TRANS': 1776} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 3.06, per 1000 atoms: 0.20 Number of scatterers: 15032 At special positions: 0 Unit cell: (109.824, 143.936, 144.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 2962 8.00 N 2590 7.00 C 9381 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 779.7 milliseconds 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3484 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 3 sheets defined 48.8% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 43 through 50 removed outlier: 3.646A pdb=" N LEU A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 54 removed outlier: 3.950A pdb=" N ILE A 54 " --> pdb=" O ILE A 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 54' Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 99 through 104 removed outlier: 4.594A pdb=" N GLU A 103 " --> pdb=" O PRO A 99 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG A 104 " --> pdb=" O PRO A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 104' Processing helix chain 'A' and resid 120 through 141 removed outlier: 3.970A pdb=" N ALA A 126 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 168 Processing helix chain 'A' and resid 175 through 192 removed outlier: 4.443A pdb=" N LEU A 179 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 removed outlier: 3.625A pdb=" N ALA A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 227 removed outlier: 3.730A pdb=" N VAL A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 removed outlier: 3.909A pdb=" N ASP A 271 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 273 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.651A pdb=" N TRP A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 298 removed outlier: 3.591A pdb=" N ILE A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASP A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE A 287 " --> pdb=" O TRP A 283 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP A 296 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 366 through 375 removed outlier: 4.097A pdb=" N TYR A 369 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 371 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP A 372 " --> pdb=" O TYR A 369 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 575 Processing helix chain 'A' and resid 581 through 586 Processing helix chain 'A' and resid 588 through 592 Processing helix chain 'A' and resid 594 through 599 removed outlier: 4.496A pdb=" N CYS A 599 " --> pdb=" O GLU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 632 Processing helix chain 'A' and resid 641 through 661 Processing helix chain 'A' and resid 672 through 684 Processing helix chain 'A' and resid 685 through 689 Processing helix chain 'A' and resid 703 through 714 Processing helix chain 'A' and resid 716 through 727 removed outlier: 4.020A pdb=" N ALA A 727 " --> pdb=" O MET A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 756 Processing helix chain 'A' and resid 757 through 785 removed outlier: 4.569A pdb=" N ASP A 780 " --> pdb=" O ALA A 776 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 816 removed outlier: 3.640A pdb=" N CYS A 807 " --> pdb=" O CYS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 852 Processing helix chain 'A' and resid 881 through 890 Processing helix chain 'A' and resid 896 through 905 Processing helix chain 'A' and resid 907 through 911 removed outlier: 4.154A pdb=" N CYS A 910 " --> pdb=" O ASP A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 961 removed outlier: 3.643A pdb=" N LYS A 961 " --> pdb=" O TYR A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 979 removed outlier: 3.593A pdb=" N CYS A 975 " --> pdb=" O ASN A 971 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1019 removed outlier: 4.170A pdb=" N ARG A1018 " --> pdb=" O THR A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1051 removed outlier: 4.218A pdb=" N THR A1051 " --> pdb=" O GLU A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1123 Processing helix chain 'A' and resid 1124 through 1132 removed outlier: 4.274A pdb=" N ASP A1128 " --> pdb=" O LYS A1124 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASN A1130 " --> pdb=" O ILE A1126 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS A1131 " --> pdb=" O TYR A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1158 removed outlier: 3.544A pdb=" N LYS A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1166 removed outlier: 4.408A pdb=" N ILE A1165 " --> pdb=" O TRP A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1181 Processing helix chain 'A' and resid 1186 through 1197 removed outlier: 3.538A pdb=" N ILE A1190 " --> pdb=" O HIS A1186 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A1191 " --> pdb=" O GLY A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1258 Processing helix chain 'A' and resid 1266 through 1271 Processing helix chain 'A' and resid 1292 through 1317 removed outlier: 4.021A pdb=" N LEU A1296 " --> pdb=" O THR A1292 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU A1298 " --> pdb=" O GLU A1294 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A1299 " --> pdb=" O LEU A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1360 Processing helix chain 'A' and resid 1369 through 1374 removed outlier: 3.804A pdb=" N GLN A1373 " --> pdb=" O ILE A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1411 removed outlier: 4.105A pdb=" N GLU A1411 " --> pdb=" O ILE A1408 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1408 through 1411' Processing helix chain 'A' and resid 1412 through 1424 removed outlier: 4.095A pdb=" N ASN A1424 " --> pdb=" O ILE A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1478 Processing helix chain 'A' and resid 1501 through 1531 removed outlier: 4.156A pdb=" N LYS A1507 " --> pdb=" O ARG A1503 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR A1508 " --> pdb=" O LYS A1504 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS A1521 " --> pdb=" O GLN A1517 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A1522 " --> pdb=" O GLU A1518 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A1524 " --> pdb=" O ASP A1520 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS A1525 " --> pdb=" O LYS A1521 " (cutoff:3.500A) Processing helix chain 'A' and resid 1534 through 1543 removed outlier: 5.057A pdb=" N GLU A1541 " --> pdb=" O ASP A1537 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN A1542 " --> pdb=" O LEU A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1544 through 1549 removed outlier: 3.953A pdb=" N SER A1548 " --> pdb=" O GLU A1545 " (cutoff:3.500A) Processing helix chain 'A' and resid 1550 through 1555 Processing helix chain 'A' and resid 1558 through 1565 Processing helix chain 'A' and resid 1567 through 1569 No H-bonds generated for 'chain 'A' and resid 1567 through 1569' Processing helix chain 'A' and resid 1570 through 1575 Processing helix chain 'A' and resid 1625 through 1630 Processing helix chain 'A' and resid 1635 through 1643 removed outlier: 4.135A pdb=" N ILE A1639 " --> pdb=" O GLU A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1674 removed outlier: 3.565A pdb=" N GLU A1653 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1704 Processing helix chain 'A' and resid 1710 through 1724 removed outlier: 4.361A pdb=" N TYR A1715 " --> pdb=" O GLU A1711 " (cutoff:3.500A) Processing helix chain 'A' and resid 1725 through 1728 Processing helix chain 'A' and resid 1730 through 1744 Processing helix chain 'A' and resid 1755 through 1776 Processing helix chain 'A' and resid 1793 through 1821 Processing helix chain 'A' and resid 1836 through 1867 Proline residue: A1851 - end of helix removed outlier: 4.221A pdb=" N ILE A1854 " --> pdb=" O ASN A1850 " (cutoff:3.500A) Processing helix chain 'A' and resid 1887 through 1897 Processing helix chain 'A' and resid 1942 through 1947 removed outlier: 3.533A pdb=" N LEU A1947 " --> pdb=" O MET A1943 " (cutoff:3.500A) Processing helix chain 'A' and resid 1951 through 1957 removed outlier: 4.138A pdb=" N HIS A1957 " --> pdb=" O LYS A1953 " (cutoff:3.500A) Processing helix chain 'A' and resid 1957 through 1985 removed outlier: 3.718A pdb=" N LEU A1985 " --> pdb=" O LYS A1981 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 568 through 570 Processing sheet with id=AA2, first strand: chain 'A' and resid 923 through 925 Processing sheet with id=AA3, first strand: chain 'A' and resid 1278 through 1279 removed outlier: 3.781A pdb=" N ARG A1285 " --> pdb=" O ASP A1279 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1638 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: 2.29 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.38: 5921 1.38 - 1.59: 9265 1.59 - 1.81: 85 1.81 - 2.02: 55 2.02 - 2.23: 4 Bond restraints: 15330 Sorted by residual: bond pdb=" CE2 PHE A 374 " pdb=" CZ PHE A 374 " ideal model delta sigma weight residual 1.382 2.227 -0.845 3.00e-02 1.11e+03 7.94e+02 bond pdb=" CD2 PHE A 374 " pdb=" CE2 PHE A 374 " ideal model delta sigma weight residual 1.382 2.225 -0.843 3.00e-02 1.11e+03 7.90e+02 bond pdb=" CE1 PHE A 374 " pdb=" CZ PHE A 374 " ideal model delta sigma weight residual 1.382 2.196 -0.814 3.00e-02 1.11e+03 7.37e+02 bond pdb=" CD1 PHE A 374 " pdb=" CE1 PHE A 374 " ideal model delta sigma weight residual 1.382 2.192 -0.810 3.00e-02 1.11e+03 7.29e+02 bond pdb=" CG PHE A 374 " pdb=" CD1 PHE A 374 " ideal model delta sigma weight residual 1.384 1.809 -0.425 2.10e-02 2.27e+03 4.09e+02 ... (remaining 15325 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.23: 20537 6.23 - 12.47: 58 12.47 - 18.70: 12 18.70 - 24.93: 1 24.93 - 31.17: 4 Bond angle restraints: 20612 Sorted by residual: angle pdb=" C GLU A1381 " pdb=" N LYS A1382 " pdb=" CA LYS A1382 " ideal model delta sigma weight residual 122.42 150.76 -28.34 1.33e+00 5.65e-01 4.54e+02 angle pdb=" C ASN A 356 " pdb=" N LYS A 357 " pdb=" CA LYS A 357 " ideal model delta sigma weight residual 122.42 153.59 -31.17 1.55e+00 4.16e-01 4.04e+02 angle pdb=" C GLN A 343 " pdb=" N GLU A 344 " pdb=" CA GLU A 344 " ideal model delta sigma weight residual 121.71 147.78 -26.07 1.39e+00 5.18e-01 3.52e+02 angle pdb=" CA ASP A1375 " pdb=" C ASP A1375 " pdb=" N ILE A1376 " ideal model delta sigma weight residual 118.04 136.04 -18.00 1.32e+00 5.74e-01 1.86e+02 angle pdb=" C GLU A 341 " pdb=" N ASN A 342 " pdb=" CA ASN A 342 " ideal model delta sigma weight residual 121.54 146.49 -24.95 1.91e+00 2.74e-01 1.71e+02 ... (remaining 20607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 8620 17.69 - 35.37: 632 35.37 - 53.06: 90 53.06 - 70.74: 16 70.74 - 88.43: 8 Dihedral angle restraints: 9366 sinusoidal: 3942 harmonic: 5424 Sorted by residual: dihedral pdb=" CA ILE A1380 " pdb=" C ILE A1380 " pdb=" N GLU A1381 " pdb=" CA GLU A1381 " ideal model delta harmonic sigma weight residual 180.00 117.07 62.93 0 5.00e+00 4.00e-02 1.58e+02 dihedral pdb=" CA ILE A1376 " pdb=" C ILE A1376 " pdb=" N LYS A1377 " pdb=" CA LYS A1377 " ideal model delta harmonic sigma weight residual 180.00 121.70 58.30 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA THR A 338 " pdb=" C THR A 338 " pdb=" N GLU A 339 " pdb=" CA GLU A 339 " ideal model delta harmonic sigma weight residual 180.00 123.19 56.81 0 5.00e+00 4.00e-02 1.29e+02 ... (remaining 9363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1952 0.075 - 0.149: 154 0.149 - 0.224: 9 0.224 - 0.298: 3 0.298 - 0.373: 3 Chirality restraints: 2121 Sorted by residual: chirality pdb=" CA LYS A 337 " pdb=" N LYS A 337 " pdb=" C LYS A 337 " pdb=" CB LYS A 337 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA ASP A1375 " pdb=" N ASP A1375 " pdb=" C ASP A1375 " pdb=" CB ASP A1375 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA GLU A1381 " pdb=" N GLU A1381 " pdb=" C GLU A1381 " pdb=" CB GLU A1381 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 2118 not shown) Planarity restraints: 2679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 374 " -0.013 2.00e-02 2.50e+03 2.39e-02 9.98e+00 pdb=" CG PHE A 374 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE A 374 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 374 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE A 374 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 PHE A 374 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 374 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1375 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C ASP A1375 " 0.047 2.00e-02 2.50e+03 pdb=" O ASP A1375 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE A1376 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 711 " -0.023 2.00e-02 2.50e+03 1.72e-02 7.41e+00 pdb=" CG TRP A 711 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP A 711 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 711 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 711 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 711 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 711 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 711 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 711 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 711 " 0.001 2.00e-02 2.50e+03 ... (remaining 2676 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 137 2.44 - 3.06: 10555 3.06 - 3.67: 22929 3.67 - 4.29: 32360 4.29 - 4.90: 52237 Nonbonded interactions: 118218 Sorted by model distance: nonbonded pdb=" O ASP A1375 " pdb=" N ILE A1379 " model vdw 1.830 3.120 nonbonded pdb=" N LYS A 357 " pdb=" CZ PHE A 374 " model vdw 1.905 3.420 nonbonded pdb=" O ASP A1375 " pdb=" N LYS A1382 " model vdw 1.920 3.120 nonbonded pdb=" N LYS A 357 " pdb=" CE2 PHE A 374 " model vdw 1.935 3.420 nonbonded pdb=" N LYS A1378 " pdb=" O GLU A1381 " model vdw 1.997 3.120 ... (remaining 118213 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 individual isotropic 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: 7.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.990 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 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 : 0.016 0.845 15330 Z= 0.761 Angle : 0.971 31.167 20612 Z= 0.597 Chirality : 0.045 0.373 2121 Planarity : 0.004 0.040 2679 Dihedral : 12.324 88.427 5882 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.84 % Favored : 88.67 % Rotamer: Outliers : 0.18 % Allowed : 0.84 % Favored : 98.98 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.20), residues: 1836 helix: 1.42 (0.19), residues: 768 sheet: -1.10 (1.55), residues: 12 loop : -2.86 (0.17), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 583 TYR 0.023 0.001 TYR A1366 PHE 0.037 0.002 PHE A 374 TRP 0.047 0.002 TRP A 711 HIS 0.004 0.001 HIS A1257 Details of bonding type rmsd covalent geometry : bond 0.01617 (15330) covalent geometry : angle 0.97112 (20612) hydrogen bonds : bond 0.13863 ( 574) hydrogen bonds : angle 4.85470 ( 1638) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.432 Fit side-chains REVERT: A 159 PHE cc_start: 0.8750 (t80) cc_final: 0.8244 (t80) REVERT: A 1404 TRP cc_start: 0.4570 (p-90) cc_final: 0.3346 (p-90) REVERT: A 1405 TRP cc_start: 0.8104 (p90) cc_final: 0.7078 (p90) REVERT: A 1412 MET cc_start: 0.8762 (mpp) cc_final: 0.8435 (mmm) REVERT: A 1781 LEU cc_start: 0.9195 (mm) cc_final: 0.8767 (tp) REVERT: A 1866 ILE cc_start: 0.8763 (tp) cc_final: 0.8492 (tp) REVERT: A 1971 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8537 (mt-10) outliers start: 3 outliers final: 0 residues processed: 100 average time/residue: 0.1228 time to fit residues: 18.6184 Evaluate side-chains 68 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 GLN A 637 ASN A 965 GLN ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1117 ASN ** A1315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1330 GLN ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1586 ASN A1847 ASN ** A1916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1972 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.135764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.101002 restraints weight = 45798.499| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 4.63 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.835 15330 Z= 0.759 Angle : 0.966 30.790 20612 Z= 0.579 Chirality : 0.046 0.369 2121 Planarity : 0.004 0.047 2679 Dihedral : 5.860 61.690 2005 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.87 % Favored : 87.58 % Rotamer: Outliers : 0.66 % Allowed : 6.95 % Favored : 92.40 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.19), residues: 1836 helix: 1.23 (0.19), residues: 798 sheet: -1.61 (1.52), residues: 12 loop : -2.87 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 991 TYR 0.019 0.001 TYR A1366 PHE 0.041 0.002 PHE A 374 TRP 0.053 0.002 TRP A 711 HIS 0.005 0.001 HIS A1709 Details of bonding type rmsd covalent geometry : bond 0.01647 (15330) covalent geometry : angle 0.96570 (20612) hydrogen bonds : bond 0.04559 ( 574) hydrogen bonds : angle 4.20110 ( 1638) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 TRP cc_start: 0.9193 (t-100) cc_final: 0.8982 (t-100) REVERT: A 718 TYR cc_start: 0.8555 (m-10) cc_final: 0.8226 (m-10) REVERT: A 1357 MET cc_start: 0.9159 (tmm) cc_final: 0.8921 (ppp) REVERT: A 1404 TRP cc_start: 0.4525 (p-90) cc_final: 0.4100 (p-90) REVERT: A 1405 TRP cc_start: 0.7969 (p90) cc_final: 0.7562 (p90) REVERT: A 1412 MET cc_start: 0.8833 (mpp) cc_final: 0.8483 (mmm) REVERT: A 1781 LEU cc_start: 0.9269 (mm) cc_final: 0.8808 (tp) REVERT: A 1866 ILE cc_start: 0.8729 (tp) cc_final: 0.8343 (tp) REVERT: A 1973 LEU cc_start: 0.9531 (mp) cc_final: 0.9142 (mm) outliers start: 11 outliers final: 6 residues processed: 85 average time/residue: 0.1136 time to fit residues: 15.1401 Evaluate side-chains 72 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 1103 TRP Chi-restraints excluded: chain A residue 1240 PHE Chi-restraints excluded: chain A residue 1916 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 143 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 101 optimal weight: 0.1980 chunk 148 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 93 optimal weight: 0.8980 chunk 135 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 GLN A 764 GLN ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.135982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.101728 restraints weight = 46217.429| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 4.67 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.835 15330 Z= 0.747 Angle : 0.935 30.899 20612 Z= 0.565 Chirality : 0.043 0.333 2121 Planarity : 0.004 0.059 2679 Dihedral : 5.765 61.023 2005 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.22 % Favored : 88.24 % Rotamer: Outliers : 0.90 % Allowed : 8.98 % Favored : 90.12 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.20), residues: 1836 helix: 1.32 (0.19), residues: 791 sheet: -1.43 (1.53), residues: 12 loop : -2.87 (0.17), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1285 TYR 0.021 0.001 TYR A1915 PHE 0.044 0.002 PHE A 374 TRP 0.050 0.002 TRP A 711 HIS 0.007 0.001 HIS A1368 Details of bonding type rmsd covalent geometry : bond 0.01617 (15330) covalent geometry : angle 0.93481 (20612) hydrogen bonds : bond 0.04163 ( 574) hydrogen bonds : angle 4.00831 ( 1638) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.7818 (t80) cc_final: 0.7571 (t80) REVERT: A 53 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7250 (mtmt) REVERT: A 215 TRP cc_start: 0.9245 (t-100) cc_final: 0.9030 (t-100) REVERT: A 224 GLU cc_start: 0.8494 (pm20) cc_final: 0.8291 (pm20) REVERT: A 718 TYR cc_start: 0.8509 (m-10) cc_final: 0.8169 (m-10) REVERT: A 1050 MET cc_start: 0.7757 (mmt) cc_final: 0.7512 (mmt) REVERT: A 1357 MET cc_start: 0.9137 (tmm) cc_final: 0.8912 (ppp) REVERT: A 1404 TRP cc_start: 0.4651 (p-90) cc_final: 0.4411 (p-90) REVERT: A 1405 TRP cc_start: 0.7880 (p90) cc_final: 0.7669 (p90) REVERT: A 1412 MET cc_start: 0.8757 (mpp) cc_final: 0.8402 (mmm) REVERT: A 1781 LEU cc_start: 0.9226 (mm) cc_final: 0.8782 (tp) REVERT: A 1866 ILE cc_start: 0.8704 (tp) cc_final: 0.8280 (tp) REVERT: A 1971 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8602 (mt-10) REVERT: A 1973 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9276 (mm) outliers start: 15 outliers final: 7 residues processed: 84 average time/residue: 0.1150 time to fit residues: 15.1496 Evaluate side-chains 74 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 1103 TRP Chi-restraints excluded: chain A residue 1240 PHE Chi-restraints excluded: chain A residue 1374 GLU Chi-restraints excluded: chain A residue 1916 ASN Chi-restraints excluded: chain A residue 1973 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 107 optimal weight: 0.0270 chunk 75 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 chunk 152 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 148 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 GLN A1302 ASN ** A1315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.135836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.101532 restraints weight = 45950.089| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 4.64 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.836 15330 Z= 0.746 Angle : 0.925 30.908 20612 Z= 0.560 Chirality : 0.043 0.335 2121 Planarity : 0.004 0.064 2679 Dihedral : 5.698 60.246 2005 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.38 % Favored : 88.07 % Rotamer: Outliers : 0.96 % Allowed : 10.06 % Favored : 88.98 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.20), residues: 1836 helix: 1.32 (0.19), residues: 806 sheet: -1.52 (1.49), residues: 12 loop : -2.88 (0.17), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 991 TYR 0.020 0.001 TYR A1366 PHE 0.045 0.002 PHE A 374 TRP 0.027 0.001 TRP A 711 HIS 0.005 0.001 HIS A1305 Details of bonding type rmsd covalent geometry : bond 0.01617 (15330) covalent geometry : angle 0.92454 (20612) hydrogen bonds : bond 0.03985 ( 574) hydrogen bonds : angle 3.92815 ( 1638) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.7681 (t80) cc_final: 0.7393 (t80) REVERT: A 215 TRP cc_start: 0.9315 (t-100) cc_final: 0.9108 (t-100) REVERT: A 718 TYR cc_start: 0.8505 (m-10) cc_final: 0.8168 (m-10) REVERT: A 993 MET cc_start: 0.0639 (mtm) cc_final: 0.0410 (mtm) REVERT: A 1044 TYR cc_start: 0.8727 (t80) cc_final: 0.8512 (t80) REVERT: A 1050 MET cc_start: 0.7900 (mmt) cc_final: 0.7567 (mmt) REVERT: A 1357 MET cc_start: 0.9113 (tmm) cc_final: 0.8899 (ppp) REVERT: A 1412 MET cc_start: 0.8748 (mpp) cc_final: 0.8393 (mmm) REVERT: A 1781 LEU cc_start: 0.9206 (mm) cc_final: 0.8745 (tp) REVERT: A 1866 ILE cc_start: 0.8668 (tp) cc_final: 0.8207 (tp) REVERT: A 1971 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8596 (mt-10) REVERT: A 1973 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9291 (mm) outliers start: 16 outliers final: 10 residues processed: 86 average time/residue: 0.1128 time to fit residues: 15.3003 Evaluate side-chains 77 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 1103 TRP Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1240 PHE Chi-restraints excluded: chain A residue 1374 GLU Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1916 ASN Chi-restraints excluded: chain A residue 1973 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 163 optimal weight: 0.3980 chunk 2 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 105 optimal weight: 0.0370 chunk 52 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 GLN ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1302 ASN ** A1315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.136593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.102069 restraints weight = 46696.333| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 4.54 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.836 15330 Z= 0.748 Angle : 0.923 30.914 20612 Z= 0.559 Chirality : 0.043 0.333 2121 Planarity : 0.004 0.067 2679 Dihedral : 5.682 60.690 2005 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.55 % Favored : 87.91 % Rotamer: Outliers : 1.44 % Allowed : 10.90 % Favored : 87.66 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.20), residues: 1836 helix: 1.32 (0.19), residues: 808 sheet: -1.58 (1.48), residues: 12 loop : -2.86 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 991 TYR 0.018 0.001 TYR A1366 PHE 0.045 0.002 PHE A 374 TRP 0.036 0.001 TRP A1404 HIS 0.004 0.001 HIS A1305 Details of bonding type rmsd covalent geometry : bond 0.01623 (15330) covalent geometry : angle 0.92267 (20612) hydrogen bonds : bond 0.03970 ( 574) hydrogen bonds : angle 3.90015 ( 1638) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 46 TYR cc_start: 0.7693 (t80) cc_final: 0.7391 (t80) REVERT: A 133 ARG cc_start: 0.8911 (tmt170) cc_final: 0.8451 (tpt170) REVERT: A 215 TRP cc_start: 0.9354 (t-100) cc_final: 0.9147 (t-100) REVERT: A 718 TYR cc_start: 0.8542 (m-10) cc_final: 0.8234 (m-10) REVERT: A 1050 MET cc_start: 0.7880 (mmt) cc_final: 0.7475 (mmt) REVERT: A 1357 MET cc_start: 0.9200 (tmm) cc_final: 0.8935 (tmm) REVERT: A 1404 TRP cc_start: 0.4166 (p-90) cc_final: 0.3467 (p-90) REVERT: A 1412 MET cc_start: 0.8730 (mpp) cc_final: 0.8388 (mmm) REVERT: A 1866 ILE cc_start: 0.8699 (tp) cc_final: 0.8231 (tp) REVERT: A 1971 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8571 (mt-10) REVERT: A 1973 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9300 (mm) outliers start: 24 outliers final: 13 residues processed: 90 average time/residue: 0.1101 time to fit residues: 15.7728 Evaluate side-chains 80 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 1103 TRP Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1240 PHE Chi-restraints excluded: chain A residue 1310 LEU Chi-restraints excluded: chain A residue 1374 GLU Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1916 ASN Chi-restraints excluded: chain A residue 1973 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 30.0000 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 0.0370 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 GLN ** A1315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.136595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.102031 restraints weight = 46298.696| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 4.49 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.836 15330 Z= 0.747 Angle : 0.923 30.921 20612 Z= 0.559 Chirality : 0.043 0.334 2121 Planarity : 0.004 0.070 2679 Dihedral : 5.656 60.316 2005 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.55 % Favored : 88.02 % Rotamer: Outliers : 1.20 % Allowed : 11.74 % Favored : 87.07 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.20), residues: 1836 helix: 1.40 (0.19), residues: 803 sheet: -1.58 (1.45), residues: 12 loop : -2.81 (0.17), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 708 TYR 0.026 0.001 TYR A1366 PHE 0.045 0.002 PHE A 374 TRP 0.025 0.001 TRP A 223 HIS 0.003 0.001 HIS A1968 Details of bonding type rmsd covalent geometry : bond 0.01620 (15330) covalent geometry : angle 0.92323 (20612) hydrogen bonds : bond 0.03918 ( 574) hydrogen bonds : angle 3.85965 ( 1638) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.7644 (t80) cc_final: 0.7414 (t80) REVERT: A 53 LYS cc_start: 0.7810 (mtpp) cc_final: 0.7228 (mtmt) REVERT: A 133 ARG cc_start: 0.8883 (tmt170) cc_final: 0.8649 (tpt90) REVERT: A 718 TYR cc_start: 0.8517 (m-10) cc_final: 0.8235 (m-10) REVERT: A 1050 MET cc_start: 0.7932 (mmt) cc_final: 0.7446 (mmt) REVERT: A 1208 THR cc_start: -0.2497 (OUTLIER) cc_final: -0.3069 (t) REVERT: A 1357 MET cc_start: 0.9187 (tmm) cc_final: 0.8930 (tmm) REVERT: A 1404 TRP cc_start: 0.4156 (p-90) cc_final: 0.3627 (p-90) REVERT: A 1412 MET cc_start: 0.8719 (mpp) cc_final: 0.8381 (mmm) REVERT: A 1866 ILE cc_start: 0.8710 (tp) cc_final: 0.8246 (tp) REVERT: A 1971 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8547 (mt-10) REVERT: A 1973 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9299 (mm) outliers start: 20 outliers final: 13 residues processed: 89 average time/residue: 0.1121 time to fit residues: 15.6752 Evaluate side-chains 81 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 1103 TRP Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1240 PHE Chi-restraints excluded: chain A residue 1374 GLU Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1916 ASN Chi-restraints excluded: chain A residue 1973 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 82 optimal weight: 7.9990 chunk 176 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 154 optimal weight: 0.6980 chunk 134 optimal weight: 0.0000 chunk 11 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 67 optimal weight: 0.0470 chunk 128 optimal weight: 5.9990 chunk 170 optimal weight: 0.7980 overall best weight: 0.4482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 GLN ** A1315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.137248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.102677 restraints weight = 46129.284| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 4.52 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.836 15330 Z= 0.744 Angle : 0.922 30.913 20612 Z= 0.557 Chirality : 0.042 0.333 2121 Planarity : 0.004 0.074 2679 Dihedral : 5.620 60.003 2005 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.95 % Favored : 88.62 % Rotamer: Outliers : 1.32 % Allowed : 12.34 % Favored : 86.35 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.20), residues: 1836 helix: 1.50 (0.19), residues: 796 sheet: -1.37 (1.49), residues: 12 loop : -2.79 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 583 TYR 0.023 0.001 TYR A1366 PHE 0.046 0.001 PHE A 374 TRP 0.032 0.001 TRP A 223 HIS 0.004 0.001 HIS A1368 Details of bonding type rmsd covalent geometry : bond 0.01613 (15330) covalent geometry : angle 0.92195 (20612) hydrogen bonds : bond 0.03778 ( 574) hydrogen bonds : angle 3.81999 ( 1638) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.7739 (t80) cc_final: 0.7385 (t80) REVERT: A 718 TYR cc_start: 0.8442 (m-10) cc_final: 0.8180 (m-10) REVERT: A 1050 MET cc_start: 0.7963 (mmt) cc_final: 0.7677 (mmt) REVERT: A 1208 THR cc_start: -0.2581 (OUTLIER) cc_final: -0.3146 (t) REVERT: A 1357 MET cc_start: 0.9200 (tmm) cc_final: 0.8942 (tmm) REVERT: A 1380 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7207 (tp) REVERT: A 1404 TRP cc_start: 0.4067 (p-90) cc_final: 0.3630 (p-90) REVERT: A 1412 MET cc_start: 0.8734 (mpp) cc_final: 0.8384 (mmm) REVERT: A 1866 ILE cc_start: 0.8625 (tp) cc_final: 0.8199 (tp) REVERT: A 1971 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8560 (mt-10) REVERT: A 1973 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9270 (mm) outliers start: 22 outliers final: 13 residues processed: 93 average time/residue: 0.1184 time to fit residues: 17.3034 Evaluate side-chains 82 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 1103 TRP Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1240 PHE Chi-restraints excluded: chain A residue 1297 LYS Chi-restraints excluded: chain A residue 1374 GLU Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1973 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 173 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 177 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 GLN A 793 ASN ** A1315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.136346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.101539 restraints weight = 46534.878| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 4.53 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.836 15330 Z= 0.749 Angle : 0.939 30.918 20612 Z= 0.564 Chirality : 0.043 0.331 2121 Planarity : 0.004 0.075 2679 Dihedral : 5.598 59.365 2005 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.55 % Favored : 88.02 % Rotamer: Outliers : 1.26 % Allowed : 12.93 % Favored : 85.81 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.20), residues: 1836 helix: 1.52 (0.19), residues: 796 sheet: -1.50 (1.41), residues: 12 loop : -2.79 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 991 TYR 0.022 0.001 TYR A1366 PHE 0.046 0.002 PHE A 374 TRP 0.035 0.001 TRP A 223 HIS 0.004 0.001 HIS A1368 Details of bonding type rmsd covalent geometry : bond 0.01626 (15330) covalent geometry : angle 0.93949 (20612) hydrogen bonds : bond 0.03855 ( 574) hydrogen bonds : angle 3.85659 ( 1638) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.7709 (t80) cc_final: 0.7376 (t80) REVERT: A 133 ARG cc_start: 0.8843 (tmt170) cc_final: 0.8636 (tpt90) REVERT: A 718 TYR cc_start: 0.8478 (m-10) cc_final: 0.8202 (m-10) REVERT: A 1050 MET cc_start: 0.7973 (mmt) cc_final: 0.7635 (mmt) REVERT: A 1357 MET cc_start: 0.9187 (tmm) cc_final: 0.8931 (tmm) REVERT: A 1404 TRP cc_start: 0.4162 (p-90) cc_final: 0.3800 (p-90) REVERT: A 1412 MET cc_start: 0.8791 (mpp) cc_final: 0.8444 (mmm) REVERT: A 1866 ILE cc_start: 0.8680 (tp) cc_final: 0.8233 (tp) REVERT: A 1971 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8562 (mt-10) REVERT: A 1973 LEU cc_start: 0.9509 (mp) cc_final: 0.9273 (mm) outliers start: 21 outliers final: 15 residues processed: 87 average time/residue: 0.1086 time to fit residues: 15.2834 Evaluate side-chains 80 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 1103 TRP Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1240 PHE Chi-restraints excluded: chain A residue 1310 LEU Chi-restraints excluded: chain A residue 1374 GLU Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1916 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 183 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 160 optimal weight: 0.0770 chunk 180 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 120 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 145 optimal weight: 0.1980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.137532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.102833 restraints weight = 46345.028| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 4.58 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.836 15330 Z= 0.745 Angle : 0.933 30.903 20612 Z= 0.560 Chirality : 0.042 0.329 2121 Planarity : 0.004 0.078 2679 Dihedral : 5.580 59.371 2005 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.62 % Favored : 88.89 % Rotamer: Outliers : 1.02 % Allowed : 13.11 % Favored : 85.87 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.20), residues: 1836 helix: 1.58 (0.19), residues: 795 sheet: -1.25 (1.49), residues: 12 loop : -2.78 (0.17), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 583 TYR 0.020 0.001 TYR A1366 PHE 0.046 0.001 PHE A 374 TRP 0.039 0.001 TRP A 223 HIS 0.004 0.001 HIS A1368 Details of bonding type rmsd covalent geometry : bond 0.01614 (15330) covalent geometry : angle 0.93260 (20612) hydrogen bonds : bond 0.03714 ( 574) hydrogen bonds : angle 3.76553 ( 1638) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 46 TYR cc_start: 0.7610 (t80) cc_final: 0.7279 (t80) REVERT: A 718 TYR cc_start: 0.8408 (m-10) cc_final: 0.8189 (m-10) REVERT: A 1050 MET cc_start: 0.7990 (mmt) cc_final: 0.7648 (mmt) REVERT: A 1357 MET cc_start: 0.9199 (tmm) cc_final: 0.8929 (tmm) REVERT: A 1404 TRP cc_start: 0.4220 (p-90) cc_final: 0.3887 (p-90) REVERT: A 1412 MET cc_start: 0.8712 (mpp) cc_final: 0.8362 (mmm) REVERT: A 1866 ILE cc_start: 0.8619 (tp) cc_final: 0.8201 (tp) REVERT: A 1971 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8542 (mt-10) REVERT: A 1973 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9255 (mm) outliers start: 17 outliers final: 13 residues processed: 83 average time/residue: 0.1061 time to fit residues: 14.2458 Evaluate side-chains 78 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 1103 TRP Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1240 PHE Chi-restraints excluded: chain A residue 1310 LEU Chi-restraints excluded: chain A residue 1374 GLU Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1973 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 181 optimal weight: 0.6980 chunk 122 optimal weight: 0.0970 chunk 87 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 GLN ** A1315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.136432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.101409 restraints weight = 46854.004| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 4.57 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.836 15330 Z= 0.749 Angle : 0.941 30.914 20612 Z= 0.565 Chirality : 0.043 0.333 2121 Planarity : 0.004 0.078 2679 Dihedral : 5.577 59.034 2005 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.55 % Favored : 87.96 % Rotamer: Outliers : 1.14 % Allowed : 13.23 % Favored : 85.63 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.20), residues: 1836 helix: 1.55 (0.19), residues: 797 sheet: -1.41 (1.43), residues: 12 loop : -2.81 (0.17), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 231 TYR 0.018 0.001 TYR A1366 PHE 0.046 0.002 PHE A 374 TRP 0.041 0.002 TRP A 223 HIS 0.003 0.001 HIS A1305 Details of bonding type rmsd covalent geometry : bond 0.01628 (15330) covalent geometry : angle 0.94112 (20612) hydrogen bonds : bond 0.03842 ( 574) hydrogen bonds : angle 3.84244 ( 1638) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.7638 (t80) cc_final: 0.7295 (t80) REVERT: A 53 LYS cc_start: 0.7431 (mtpt) cc_final: 0.6997 (mtpp) REVERT: A 718 TYR cc_start: 0.8450 (m-10) cc_final: 0.8214 (m-10) REVERT: A 853 ARG cc_start: 0.7914 (mmm160) cc_final: 0.7667 (mmm160) REVERT: A 1050 MET cc_start: 0.7998 (mmt) cc_final: 0.7620 (mmt) REVERT: A 1357 MET cc_start: 0.9201 (tmm) cc_final: 0.8947 (tmm) REVERT: A 1404 TRP cc_start: 0.4259 (p-90) cc_final: 0.3910 (p-90) REVERT: A 1412 MET cc_start: 0.8827 (mpp) cc_final: 0.8479 (mmm) REVERT: A 1866 ILE cc_start: 0.8691 (tp) cc_final: 0.8243 (tp) REVERT: A 1971 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8560 (mt-10) REVERT: A 1973 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9277 (mm) outliers start: 19 outliers final: 13 residues processed: 83 average time/residue: 0.1245 time to fit residues: 15.8703 Evaluate side-chains 79 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1240 PHE Chi-restraints excluded: chain A residue 1297 LYS Chi-restraints excluded: chain A residue 1310 LEU Chi-restraints excluded: chain A residue 1374 GLU Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1973 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 144 optimal weight: 0.9980 chunk 79 optimal weight: 0.3980 chunk 24 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 143 optimal weight: 0.4980 chunk 38 optimal weight: 8.9990 chunk 158 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 GLN ** A1315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.136950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.102272 restraints weight = 46442.854| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 4.53 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.837 15330 Z= 0.746 Angle : 0.936 30.908 20612 Z= 0.561 Chirality : 0.042 0.331 2121 Planarity : 0.004 0.080 2679 Dihedral : 5.554 59.159 2005 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.73 % Favored : 88.78 % Rotamer: Outliers : 0.96 % Allowed : 13.47 % Favored : 85.57 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.20), residues: 1836 helix: 1.61 (0.19), residues: 791 sheet: -1.31 (1.46), residues: 12 loop : -2.79 (0.17), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 231 TYR 0.018 0.001 TYR A1915 PHE 0.046 0.002 PHE A 374 TRP 0.040 0.001 TRP A 223 HIS 0.003 0.001 HIS A1968 Details of bonding type rmsd covalent geometry : bond 0.01618 (15330) covalent geometry : angle 0.93586 (20612) hydrogen bonds : bond 0.03770 ( 574) hydrogen bonds : angle 3.79882 ( 1638) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4020.63 seconds wall clock time: 69 minutes 57.63 seconds (4197.63 seconds total)