Starting phenix.real_space_refine on Sat Aug 23 12:19:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wl6_37612/08_2025/8wl6_37612.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wl6_37612/08_2025/8wl6_37612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wl6_37612/08_2025/8wl6_37612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wl6_37612/08_2025/8wl6_37612.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wl6_37612/08_2025/8wl6_37612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wl6_37612/08_2025/8wl6_37612.map" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 7783 2.51 5 N 1998 2.21 5 O 2068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11922 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 11922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1489, 11922 Classifications: {'peptide': 1489} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 66, 'TRANS': 1422} Chain breaks: 8 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 5, 'GLU:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 5, 'PHE:plan': 5, 'ARG:plan': 8, 'TRP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 161 Time building chain proxies: 3.13, per 1000 atoms: 0.26 Number of scatterers: 11922 At special positions: 0 Unit cell: (112.2, 118.8, 132, 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 73 16.00 O 2068 8.00 N 1998 7.00 C 7783 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1328 " - pdb=" SG CYS A1345 " distance=2.03 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: 1.01 Conformation dependent library (CDL) restraints added in 571.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2942 Ramachandran restraints generated. 1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2828 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 2 sheets defined 64.8% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 148 through 153 removed outlier: 3.518A pdb=" N THR A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 removed outlier: 3.561A pdb=" N ILE A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 197 removed outlier: 3.635A pdb=" N MET A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 214 removed outlier: 3.883A pdb=" N LEU A 206 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 3.972A pdb=" N LYS A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 242 removed outlier: 3.556A pdb=" N ILE A 236 " --> pdb=" O MET A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.646A pdb=" N LEU A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 3.626A pdb=" N LYS A 275 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 277 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.946A pdb=" N ALA A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 313 Processing helix chain 'A' and resid 317 through 320 removed outlier: 3.573A pdb=" N PHE A 320 " --> pdb=" O GLN A 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 317 through 320' Processing helix chain 'A' and resid 321 through 338 removed outlier: 3.657A pdb=" N LEU A 325 " --> pdb=" O THR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 369 removed outlier: 3.509A pdb=" N ASN A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) Proline residue: A 360 - end of helix removed outlier: 3.812A pdb=" N VAL A 369 " --> pdb=" O ILE A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 399 removed outlier: 4.150A pdb=" N TYR A 399 " --> pdb=" O GLN A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.737A pdb=" N ILE A 403 " --> pdb=" O TYR A 399 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 404 " --> pdb=" O PRO A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 399 through 404' Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 444 through 452 removed outlier: 3.502A pdb=" N LEU A 448 " --> pdb=" O THR A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 470 Processing helix chain 'A' and resid 489 through 518 removed outlier: 3.673A pdb=" N VAL A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 551 Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 561 through 583 Processing helix chain 'A' and resid 615 through 654 removed outlier: 4.347A pdb=" N TRP A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) Proline residue: A 647 - end of helix removed outlier: 3.743A pdb=" N THR A 654 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 711 removed outlier: 3.716A pdb=" N LYS A 670 " --> pdb=" O ALA A 666 " (cutoff:3.500A) Proline residue: A 673 - end of helix removed outlier: 4.058A pdb=" N LEU A 677 " --> pdb=" O PRO A 673 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY A 678 " --> pdb=" O LYS A 674 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 679 " --> pdb=" O ILE A 675 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 680 " --> pdb=" O VAL A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 removed outlier: 4.068A pdb=" N ILE A 722 " --> pdb=" O PRO A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 734 removed outlier: 3.624A pdb=" N ARG A 729 " --> pdb=" O ARG A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 764 removed outlier: 3.973A pdb=" N GLU A 764 " --> pdb=" O SER A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 776 removed outlier: 4.180A pdb=" N GLN A 773 " --> pdb=" O ILE A 769 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A 774 " --> pdb=" O ASP A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 3.943A pdb=" N PHE A 804 " --> pdb=" O ASP A 801 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU A 805 " --> pdb=" O ASN A 802 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 801 through 805' Processing helix chain 'A' and resid 820 through 826 Processing helix chain 'A' and resid 835 through 839 Processing helix chain 'A' and resid 856 through 862 removed outlier: 3.645A pdb=" N ILE A 860 " --> pdb=" O SER A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 879 Processing helix chain 'A' and resid 882 through 892 Processing helix chain 'A' and resid 932 through 945 Processing helix chain 'A' and resid 949 through 958 removed outlier: 3.765A pdb=" N THR A 953 " --> pdb=" O THR A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 972 removed outlier: 4.352A pdb=" N ARG A 962 " --> pdb=" O MET A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 980 removed outlier: 4.215A pdb=" N GLN A 977 " --> pdb=" O PRO A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 997 removed outlier: 3.635A pdb=" N LEU A 990 " --> pdb=" O LEU A 986 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 997 " --> pdb=" O MET A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1025 Processing helix chain 'A' and resid 1081 through 1090 removed outlier: 3.585A pdb=" N ALA A1089 " --> pdb=" O ASN A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1093 No H-bonds generated for 'chain 'A' and resid 1091 through 1093' Processing helix chain 'A' and resid 1108 through 1113 removed outlier: 3.961A pdb=" N LEU A1113 " --> pdb=" O GLU A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1120 Processing helix chain 'A' and resid 1121 through 1123 No H-bonds generated for 'chain 'A' and resid 1121 through 1123' Processing helix chain 'A' and resid 1201 through 1206 removed outlier: 3.798A pdb=" N THR A1206 " --> pdb=" O THR A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1233 removed outlier: 3.697A pdb=" N GLY A1226 " --> pdb=" O ASP A1222 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A1233 " --> pdb=" O ALA A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1268 Processing helix chain 'A' and resid 1272 through 1280 removed outlier: 3.869A pdb=" N TYR A1276 " --> pdb=" O SER A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1292 Processing helix chain 'A' and resid 1293 through 1325 removed outlier: 4.145A pdb=" N PHE A1297 " --> pdb=" O ALA A1293 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N HIS A1298 " --> pdb=" O HIS A1294 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN A1305 " --> pdb=" O ASN A1301 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A1306 " --> pdb=" O LEU A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1378 removed outlier: 4.001A pdb=" N VAL A1352 " --> pdb=" O PHE A1348 " (cutoff:3.500A) Proline residue: A1372 - end of helix Processing helix chain 'A' and resid 1379 through 1390 Processing helix chain 'A' and resid 1437 through 1467 removed outlier: 3.804A pdb=" N LEU A1441 " --> pdb=" O PRO A1437 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N MET A1452 " --> pdb=" O SER A1448 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG A1455 " --> pdb=" O TYR A1451 " (cutoff:3.500A) Processing helix chain 'A' and resid 1471 through 1490 removed outlier: 3.632A pdb=" N ALA A1477 " --> pdb=" O LEU A1473 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A1478 " --> pdb=" O TRP A1474 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU A1479 " --> pdb=" O PHE A1475 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER A1480 " --> pdb=" O TRP A1476 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER A1481 " --> pdb=" O ALA A1477 " (cutoff:3.500A) Proline residue: A1486 - end of helix Processing helix chain 'A' and resid 1495 through 1518 Processing helix chain 'A' and resid 1556 through 1583 removed outlier: 3.793A pdb=" N LEU A1560 " --> pdb=" O HIS A1556 " (cutoff:3.500A) Proline residue: A1567 - end of helix removed outlier: 3.690A pdb=" N ASN A1583 " --> pdb=" O PHE A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1597 through 1627 removed outlier: 3.890A pdb=" N ARG A1601 " --> pdb=" O ASN A1597 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE A1603 " --> pdb=" O VAL A1599 " (cutoff:3.500A) Proline residue: A1609 - end of helix removed outlier: 3.787A pdb=" N VAL A1616 " --> pdb=" O VAL A1612 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A1617 " --> pdb=" O ASN A1613 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1665 removed outlier: 3.777A pdb=" N GLU A1665 " --> pdb=" O MET A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1696 removed outlier: 3.746A pdb=" N MET A1672 " --> pdb=" O ASN A1668 " (cutoff:3.500A) Processing helix chain 'A' and resid 1723 through 1759 Proline residue: A1756 - end of helix removed outlier: 4.180A pdb=" N ILE A1759 " --> pdb=" O LEU A1755 " (cutoff:3.500A) Processing helix chain 'A' and resid 1765 through 1779 Proline residue: A1776 - end of helix Processing helix chain 'A' and resid 1790 through 1825 Proline residue: A1818 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 373 Processing sheet with id=AA2, first strand: chain 'A' and resid 1068 through 1069 removed outlier: 4.217A pdb=" N PHE A1068 " --> pdb=" O LEU A1051 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A1051 " --> pdb=" O PHE A1068 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG A1046 " --> pdb=" O GLU A1036 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A1036 " --> pdb=" O ARG A1046 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP A1034 " --> pdb=" O TYR A1048 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A1029 " --> pdb=" O PHE A1000 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A1033 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE A 842 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU A1001 " --> pdb=" O PHE A 842 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL A 844 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N SER A1003 " --> pdb=" O VAL A 844 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A 846 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ALA A1149 " --> pdb=" O ASN A1200 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL A1148 " --> pdb=" O ARG A1235 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LYS A1237 " --> pdb=" O VAL A1148 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE A1150 " --> pdb=" O LYS A1237 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N CYS A1239 " --> pdb=" O ILE A1150 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLY A1152 " --> pdb=" O CYS A1239 " (cutoff:3.500A) 641 hydrogen bonds defined for protein. 1896 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: 2.12 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3742 1.34 - 1.46: 2984 1.46 - 1.58: 5396 1.58 - 1.70: 0 1.70 - 1.82: 116 Bond restraints: 12238 Sorted by residual: bond pdb=" C LEU A 642 " pdb=" O LEU A 642 " ideal model delta sigma weight residual 1.237 1.259 -0.023 1.16e-02 7.43e+03 3.87e+00 bond pdb=" CA VAL A1371 " pdb=" C VAL A1371 " ideal model delta sigma weight residual 1.520 1.533 -0.013 8.80e-03 1.29e+04 2.24e+00 bond pdb=" C PHE A 685 " pdb=" O PHE A 685 " ideal model delta sigma weight residual 1.236 1.253 -0.017 1.15e-02 7.56e+03 2.15e+00 bond pdb=" CA VAL A1371 " pdb=" CB VAL A1371 " ideal model delta sigma weight residual 1.534 1.544 -0.009 6.80e-03 2.16e+04 1.84e+00 bond pdb=" CA ASP A 646 " pdb=" C ASP A 646 " ideal model delta sigma weight residual 1.524 1.540 -0.017 1.26e-02 6.30e+03 1.74e+00 ... (remaining 12233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 16414 2.27 - 4.55: 173 4.55 - 6.82: 25 6.82 - 9.09: 5 9.09 - 11.36: 1 Bond angle restraints: 16618 Sorted by residual: angle pdb=" N PRO A1782 " pdb=" CA PRO A1782 " pdb=" CB PRO A1782 " ideal model delta sigma weight residual 103.08 111.50 -8.42 9.70e-01 1.06e+00 7.54e+01 angle pdb=" N PRO A1783 " pdb=" CA PRO A1783 " pdb=" CB PRO A1783 " ideal model delta sigma weight residual 103.25 110.54 -7.29 1.05e+00 9.07e-01 4.82e+01 angle pdb=" N PRO A 810 " pdb=" CA PRO A 810 " pdb=" CB PRO A 810 " ideal model delta sigma weight residual 103.25 109.91 -6.66 1.05e+00 9.07e-01 4.02e+01 angle pdb=" N PRO A1776 " pdb=" CA PRO A1776 " pdb=" CB PRO A1776 " ideal model delta sigma weight residual 103.39 110.20 -6.81 1.08e+00 8.57e-01 3.97e+01 angle pdb=" CA PRO A 647 " pdb=" N PRO A 647 " pdb=" CD PRO A 647 " ideal model delta sigma weight residual 112.00 105.58 6.42 1.40e+00 5.10e-01 2.10e+01 ... (remaining 16613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6185 17.98 - 35.96: 772 35.96 - 53.93: 204 53.93 - 71.91: 28 71.91 - 89.89: 8 Dihedral angle restraints: 7197 sinusoidal: 2821 harmonic: 4376 Sorted by residual: dihedral pdb=" CA TYR A 662 " pdb=" C TYR A 662 " pdb=" N TRP A 663 " pdb=" CA TRP A 663 " ideal model delta harmonic sigma weight residual 180.00 157.52 22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ALA A 551 " pdb=" C ALA A 551 " pdb=" N TYR A 552 " pdb=" CA TYR A 552 " ideal model delta harmonic sigma weight residual 180.00 158.99 21.01 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA TYR A 552 " pdb=" C TYR A 552 " pdb=" N ASP A 553 " pdb=" CA ASP A 553 " ideal model delta harmonic sigma weight residual 180.00 159.72 20.28 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 7194 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1414 0.046 - 0.091: 355 0.091 - 0.137: 70 0.137 - 0.183: 2 0.183 - 0.229: 4 Chirality restraints: 1845 Sorted by residual: chirality pdb=" CA PRO A1776 " pdb=" N PRO A1776 " pdb=" C PRO A1776 " pdb=" CB PRO A1776 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA PRO A 810 " pdb=" N PRO A 810 " pdb=" C PRO A 810 " pdb=" CB PRO A 810 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA PRO A1783 " pdb=" N PRO A1783 " pdb=" C PRO A1783 " pdb=" CB PRO A1783 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1842 not shown) Planarity restraints: 2087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 646 " 0.074 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO A 647 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO A 647 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 647 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1447 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C GLY A1447 " 0.044 2.00e-02 2.50e+03 pdb=" O GLY A1447 " -0.017 2.00e-02 2.50e+03 pdb=" N SER A1448 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A1817 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO A1818 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A1818 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1818 " 0.031 5.00e-02 4.00e+02 ... (remaining 2084 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1149 2.74 - 3.28: 11536 3.28 - 3.82: 19044 3.82 - 4.36: 20407 4.36 - 4.90: 36089 Nonbonded interactions: 88225 Sorted by model distance: nonbonded pdb=" O PHE A 887 " pdb=" OG1 THR A 891 " model vdw 2.204 3.040 nonbonded pdb=" O SER A 603 " pdb=" OG1 THR A 607 " model vdw 2.248 3.040 nonbonded pdb=" OG1 THR A1040 " pdb=" OE1 GLU A1041 " model vdw 2.254 3.040 nonbonded pdb=" O ILE A 648 " pdb=" OG SER A 652 " model vdw 2.291 3.040 nonbonded pdb=" O ASP A 374 " pdb=" NH1 ARG A 376 " model vdw 2.324 3.120 ... (remaining 88220 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: 1.260 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.860 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 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 : 0.003 0.059 12239 Z= 0.168 Angle : 0.618 11.363 16620 Z= 0.350 Chirality : 0.042 0.229 1845 Planarity : 0.005 0.109 2087 Dihedral : 16.842 89.891 4366 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.64 % Favored : 94.09 % Rotamer: Outliers : 0.32 % Allowed : 25.02 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.22), residues: 1471 helix: 1.34 (0.18), residues: 847 sheet: 0.06 (0.82), residues: 37 loop : -1.75 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1332 TYR 0.014 0.001 TYR A1292 PHE 0.024 0.001 PHE A 685 TRP 0.016 0.001 TRP A1474 HIS 0.006 0.001 HIS A1838 Details of bonding type rmsd covalent geometry : bond 0.00343 (12238) covalent geometry : angle 0.61765 (16618) SS BOND : bond 0.00060 ( 1) SS BOND : angle 0.76118 ( 2) hydrogen bonds : bond 0.14199 ( 641) hydrogen bonds : angle 4.91448 ( 1896) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2942 Ramachandran restraints generated. 1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2942 Ramachandran restraints generated. 1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 777 TYR cc_start: 0.5355 (OUTLIER) cc_final: 0.3584 (t80) REVERT: A 1597 ASN cc_start: 0.8165 (t0) cc_final: 0.7913 (t0) outliers start: 4 outliers final: 1 residues processed: 122 average time/residue: 0.1230 time to fit residues: 21.2886 Evaluate side-chains 118 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 1148 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 317 GLN A 384 HIS A 771 HIS A1748 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.215645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3885 r_free = 0.3885 target = 0.158810 restraints weight = 13318.784| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.72 r_work: 0.3521 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12239 Z= 0.224 Angle : 0.651 9.437 16620 Z= 0.346 Chirality : 0.043 0.182 1845 Planarity : 0.005 0.073 2087 Dihedral : 4.855 47.839 1632 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.53 % Allowed : 23.98 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.22), residues: 1471 helix: 1.12 (0.18), residues: 853 sheet: -0.66 (0.90), residues: 35 loop : -1.69 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1094 TYR 0.022 0.002 TYR A1276 PHE 0.031 0.002 PHE A 517 TRP 0.014 0.002 TRP A 625 HIS 0.007 0.001 HIS A1323 Details of bonding type rmsd covalent geometry : bond 0.00510 (12238) covalent geometry : angle 0.65114 (16618) SS BOND : bond 0.00216 ( 1) SS BOND : angle 0.33308 ( 2) hydrogen bonds : bond 0.09637 ( 641) hydrogen bonds : angle 4.75968 ( 1896) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2942 Ramachandran restraints generated. 1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2942 Ramachandran restraints generated. 1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 GLN cc_start: 0.7986 (mm110) cc_final: 0.7474 (mt0) REVERT: A 317 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8162 (mt0) REVERT: A 713 ILE cc_start: 0.3560 (OUTLIER) cc_final: 0.2829 (tp) REVERT: A 716 LEU cc_start: 0.1064 (OUTLIER) cc_final: 0.0536 (pp) REVERT: A 777 TYR cc_start: 0.4750 (OUTLIER) cc_final: 0.2725 (t80) REVERT: A 975 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.7083 (mm) REVERT: A 1137 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7855 (pp) REVERT: A 1368 ILE cc_start: 0.5972 (OUTLIER) cc_final: 0.5729 (tp) REVERT: A 1597 ASN cc_start: 0.8652 (t0) cc_final: 0.8220 (t0) REVERT: A 1603 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7886 (tt) outliers start: 44 outliers final: 18 residues processed: 157 average time/residue: 0.1179 time to fit residues: 26.3990 Evaluate side-chains 149 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1192 HIS Chi-restraints excluded: chain A residue 1204 MET Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1586 THR Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1689 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 77 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 0.0870 chunk 108 optimal weight: 0.3980 chunk 70 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 134 optimal weight: 0.6980 chunk 143 optimal weight: 9.9990 chunk 69 optimal weight: 0.3980 chunk 140 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 317 GLN A 384 HIS A 721 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.222764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.163969 restraints weight = 13448.455| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 5.93 r_work: 0.3464 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12239 Z= 0.131 Angle : 0.534 9.234 16620 Z= 0.281 Chirality : 0.039 0.137 1845 Planarity : 0.004 0.059 2087 Dihedral : 4.447 48.998 1632 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.05 % Allowed : 24.78 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.23), residues: 1471 helix: 1.53 (0.18), residues: 855 sheet: -0.02 (0.90), residues: 32 loop : -1.70 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 376 TYR 0.012 0.001 TYR A1800 PHE 0.015 0.001 PHE A 685 TRP 0.015 0.001 TRP A 456 HIS 0.003 0.000 HIS A 563 Details of bonding type rmsd covalent geometry : bond 0.00247 (12238) covalent geometry : angle 0.53431 (16618) SS BOND : bond 0.00083 ( 1) SS BOND : angle 0.65324 ( 2) hydrogen bonds : bond 0.06753 ( 641) hydrogen bonds : angle 4.39553 ( 1896) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2942 Ramachandran restraints generated. 1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2942 Ramachandran restraints generated. 1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 GLN cc_start: 0.7941 (mm110) cc_final: 0.7424 (mt0) REVERT: A 317 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: A 713 ILE cc_start: 0.3464 (OUTLIER) cc_final: 0.2833 (tp) REVERT: A 716 LEU cc_start: 0.1142 (OUTLIER) cc_final: 0.0762 (pp) REVERT: A 777 TYR cc_start: 0.4286 (OUTLIER) cc_final: 0.2505 (t80) REVERT: A 1571 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.7178 (m-80) REVERT: A 1589 LYS cc_start: 0.3266 (tppt) cc_final: 0.2074 (tptp) REVERT: A 1597 ASN cc_start: 0.8414 (t0) cc_final: 0.8094 (t0) outliers start: 38 outliers final: 15 residues processed: 152 average time/residue: 0.1201 time to fit residues: 25.9460 Evaluate side-chains 137 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1192 HIS Chi-restraints excluded: chain A residue 1204 MET Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1571 TYR Chi-restraints excluded: chain A residue 1586 THR Chi-restraints excluded: chain A residue 1655 ILE Chi-restraints excluded: chain A residue 1694 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 3 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 114 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.218477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.159817 restraints weight = 13340.927| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 6.77 r_work: 0.3392 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12239 Z= 0.167 Angle : 0.581 10.156 16620 Z= 0.306 Chirality : 0.041 0.228 1845 Planarity : 0.005 0.054 2087 Dihedral : 4.492 50.321 1632 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.77 % Allowed : 24.22 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.23), residues: 1471 helix: 1.43 (0.18), residues: 857 sheet: -0.48 (0.91), residues: 34 loop : -1.65 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 376 TYR 0.017 0.001 TYR A1276 PHE 0.023 0.001 PHE A 517 TRP 0.012 0.001 TRP A 625 HIS 0.004 0.001 HIS A1323 Details of bonding type rmsd covalent geometry : bond 0.00364 (12238) covalent geometry : angle 0.58105 (16618) SS BOND : bond 0.00214 ( 1) SS BOND : angle 0.35836 ( 2) hydrogen bonds : bond 0.07928 ( 641) hydrogen bonds : angle 4.45339 ( 1896) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2942 Ramachandran restraints generated. 1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2942 Ramachandran restraints generated. 1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 116 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 156 GLN cc_start: 0.8086 (mm110) cc_final: 0.7471 (mt0) REVERT: A 475 TYR cc_start: 0.7211 (OUTLIER) cc_final: 0.6732 (p90) REVERT: A 716 LEU cc_start: 0.0751 (OUTLIER) cc_final: 0.0355 (pp) REVERT: A 777 TYR cc_start: 0.4077 (OUTLIER) cc_final: 0.2375 (t80) REVERT: A 1451 TYR cc_start: 0.7493 (OUTLIER) cc_final: 0.6519 (t80) REVERT: A 1571 TYR cc_start: 0.7671 (OUTLIER) cc_final: 0.6965 (m-80) REVERT: A 1589 LYS cc_start: 0.2713 (tppt) cc_final: 0.2308 (tppt) REVERT: A 1597 ASN cc_start: 0.8530 (t0) cc_final: 0.8065 (t0) REVERT: A 1603 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7704 (tt) outliers start: 47 outliers final: 23 residues processed: 155 average time/residue: 0.1024 time to fit residues: 23.1134 Evaluate side-chains 145 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1192 HIS Chi-restraints excluded: chain A residue 1204 MET Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1451 TYR Chi-restraints excluded: chain A residue 1562 MET Chi-restraints excluded: chain A residue 1571 TYR Chi-restraints excluded: chain A residue 1586 THR Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1689 CYS Chi-restraints excluded: chain A residue 1694 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 16 optimal weight: 0.6980 chunk 92 optimal weight: 0.0010 chunk 88 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.223334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.153760 restraints weight = 13121.578| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 3.36 r_work: 0.3541 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12239 Z= 0.127 Angle : 0.534 8.832 16620 Z= 0.277 Chirality : 0.039 0.167 1845 Planarity : 0.004 0.051 2087 Dihedral : 4.241 51.240 1632 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.89 % Allowed : 25.02 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.23), residues: 1471 helix: 1.76 (0.18), residues: 850 sheet: -0.10 (0.93), residues: 32 loop : -1.62 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1795 TYR 0.011 0.001 TYR A1276 PHE 0.013 0.001 PHE A1766 TRP 0.013 0.001 TRP A 456 HIS 0.004 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00251 (12238) covalent geometry : angle 0.53362 (16618) SS BOND : bond 0.00082 ( 1) SS BOND : angle 0.62789 ( 2) hydrogen bonds : bond 0.06179 ( 641) hydrogen bonds : angle 4.28049 ( 1896) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2942 Ramachandran restraints generated. 1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2942 Ramachandran restraints generated. 1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 156 GLN cc_start: 0.7990 (mm110) cc_final: 0.7535 (mt0) REVERT: A 475 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.6748 (p90) REVERT: A 492 LYS cc_start: 0.2960 (OUTLIER) cc_final: 0.2747 (mtmm) REVERT: A 620 MET cc_start: 0.6859 (tpt) cc_final: 0.6497 (mmt) REVERT: A 663 TRP cc_start: 0.7302 (OUTLIER) cc_final: 0.6442 (m-10) REVERT: A 713 ILE cc_start: 0.4213 (OUTLIER) cc_final: 0.3500 (tp) REVERT: A 716 LEU cc_start: 0.0786 (OUTLIER) cc_final: 0.0349 (pp) REVERT: A 777 TYR cc_start: 0.4091 (OUTLIER) cc_final: 0.2217 (t80) REVERT: A 1451 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.6511 (t80) REVERT: A 1571 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.7279 (m-80) REVERT: A 1589 LYS cc_start: 0.2772 (tppt) cc_final: 0.2079 (tppt) REVERT: A 1770 MET cc_start: 0.6576 (mmm) cc_final: 0.6211 (mpp) outliers start: 36 outliers final: 24 residues processed: 150 average time/residue: 0.1267 time to fit residues: 27.0146 Evaluate side-chains 145 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 443 ARG Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1192 HIS Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1451 TYR Chi-restraints excluded: chain A residue 1562 MET Chi-restraints excluded: chain A residue 1571 TYR Chi-restraints excluded: chain A residue 1586 THR Chi-restraints excluded: chain A residue 1694 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 55 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.220510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.172064 restraints weight = 13446.403| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 4.13 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12239 Z= 0.143 Angle : 0.556 8.861 16620 Z= 0.289 Chirality : 0.040 0.187 1845 Planarity : 0.004 0.052 2087 Dihedral : 4.291 52.284 1632 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.77 % Allowed : 24.46 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.23), residues: 1471 helix: 1.62 (0.18), residues: 865 sheet: -0.56 (0.93), residues: 34 loop : -1.59 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 376 TYR 0.014 0.001 TYR A1276 PHE 0.019 0.001 PHE A 517 TRP 0.011 0.001 TRP A 625 HIS 0.005 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00302 (12238) covalent geometry : angle 0.55616 (16618) SS BOND : bond 0.00162 ( 1) SS BOND : angle 0.43208 ( 2) hydrogen bonds : bond 0.06950 ( 641) hydrogen bonds : angle 4.30651 ( 1896) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2942 Ramachandran restraints generated. 1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2942 Ramachandran restraints generated. 1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 0.460 Fit side-chains REVERT: A 156 GLN cc_start: 0.7951 (mm110) cc_final: 0.7705 (mt0) REVERT: A 475 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.6740 (p90) REVERT: A 620 MET cc_start: 0.6543 (tpt) cc_final: 0.6280 (mmt) REVERT: A 663 TRP cc_start: 0.7252 (OUTLIER) cc_final: 0.6488 (m-10) REVERT: A 713 ILE cc_start: 0.4283 (OUTLIER) cc_final: 0.3972 (tp) REVERT: A 716 LEU cc_start: 0.1484 (OUTLIER) cc_final: 0.0807 (pp) REVERT: A 722 ILE cc_start: 0.5109 (OUTLIER) cc_final: 0.4796 (tp) REVERT: A 777 TYR cc_start: 0.4881 (OUTLIER) cc_final: 0.2979 (t80) REVERT: A 1308 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.6923 (mm) REVERT: A 1451 TYR cc_start: 0.6810 (OUTLIER) cc_final: 0.6581 (t80) REVERT: A 1571 TYR cc_start: 0.7775 (OUTLIER) cc_final: 0.7372 (m-80) REVERT: A 1589 LYS cc_start: 0.3441 (tppt) cc_final: 0.2777 (tppt) REVERT: A 1597 ASN cc_start: 0.8340 (t0) cc_final: 0.8039 (t0) outliers start: 47 outliers final: 26 residues processed: 156 average time/residue: 0.1065 time to fit residues: 23.7351 Evaluate side-chains 147 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1204 MET Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1451 TYR Chi-restraints excluded: chain A residue 1562 MET Chi-restraints excluded: chain A residue 1571 TYR Chi-restraints excluded: chain A residue 1586 THR Chi-restraints excluded: chain A residue 1689 CYS Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1694 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 84 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 70 optimal weight: 30.0000 chunk 124 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.221620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.162651 restraints weight = 13310.585| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 5.88 r_work: 0.3454 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12239 Z= 0.136 Angle : 0.560 14.050 16620 Z= 0.288 Chirality : 0.040 0.189 1845 Planarity : 0.004 0.051 2087 Dihedral : 4.265 53.294 1632 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.53 % Allowed : 24.86 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.23), residues: 1471 helix: 1.75 (0.18), residues: 856 sheet: -0.58 (0.93), residues: 34 loop : -1.55 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 376 TYR 0.013 0.001 TYR A1276 PHE 0.016 0.001 PHE A 517 TRP 0.011 0.001 TRP A 625 HIS 0.005 0.001 HIS A1767 Details of bonding type rmsd covalent geometry : bond 0.00280 (12238) covalent geometry : angle 0.55956 (16618) SS BOND : bond 0.00113 ( 1) SS BOND : angle 0.50562 ( 2) hydrogen bonds : bond 0.06649 ( 641) hydrogen bonds : angle 4.28746 ( 1896) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2942 Ramachandran restraints generated. 1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2942 Ramachandran restraints generated. 1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 115 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 156 GLN cc_start: 0.8094 (mm110) cc_final: 0.7612 (mt0) REVERT: A 311 CYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8205 (m) REVERT: A 475 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.6686 (p90) REVERT: A 620 MET cc_start: 0.7002 (tpt) cc_final: 0.6762 (mmt) REVERT: A 663 TRP cc_start: 0.7347 (OUTLIER) cc_final: 0.6677 (m-10) REVERT: A 713 ILE cc_start: 0.3858 (OUTLIER) cc_final: 0.3517 (tp) REVERT: A 716 LEU cc_start: 0.0453 (OUTLIER) cc_final: 0.0077 (pp) REVERT: A 722 ILE cc_start: 0.5015 (OUTLIER) cc_final: 0.4640 (tp) REVERT: A 777 TYR cc_start: 0.3701 (OUTLIER) cc_final: 0.3179 (t80) REVERT: A 1308 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7330 (mm) REVERT: A 1451 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.6557 (t80) REVERT: A 1571 TYR cc_start: 0.7677 (OUTLIER) cc_final: 0.7115 (m-80) REVERT: A 1589 LYS cc_start: 0.2497 (tppt) cc_final: 0.1741 (tppt) REVERT: A 1597 ASN cc_start: 0.8426 (t0) cc_final: 0.7897 (t0) REVERT: A 1603 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7635 (tt) REVERT: A 1770 MET cc_start: 0.6964 (mpp) cc_final: 0.6024 (tpt) outliers start: 44 outliers final: 27 residues processed: 151 average time/residue: 0.1216 time to fit residues: 26.3801 Evaluate side-chains 150 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1192 HIS Chi-restraints excluded: chain A residue 1204 MET Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1451 TYR Chi-restraints excluded: chain A residue 1562 MET Chi-restraints excluded: chain A residue 1571 TYR Chi-restraints excluded: chain A residue 1586 THR Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1689 CYS Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1694 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 45 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 70 optimal weight: 30.0000 chunk 36 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 848 HIS A1129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.220200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.164535 restraints weight = 13342.088| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 1.73 r_work: 0.3587 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12239 Z= 0.146 Angle : 0.567 10.150 16620 Z= 0.293 Chirality : 0.040 0.173 1845 Planarity : 0.004 0.051 2087 Dihedral : 4.283 54.611 1632 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.77 % Allowed : 24.54 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.23), residues: 1471 helix: 1.68 (0.18), residues: 859 sheet: -0.64 (0.92), residues: 34 loop : -1.55 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 376 TYR 0.015 0.001 TYR A1276 PHE 0.019 0.001 PHE A 517 TRP 0.011 0.001 TRP A 625 HIS 0.004 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00307 (12238) covalent geometry : angle 0.56665 (16618) SS BOND : bond 0.00139 ( 1) SS BOND : angle 0.41561 ( 2) hydrogen bonds : bond 0.07052 ( 641) hydrogen bonds : angle 4.30959 ( 1896) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2942 Ramachandran restraints generated. 1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2942 Ramachandran restraints generated. 1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 113 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 156 GLN cc_start: 0.8120 (mm110) cc_final: 0.7662 (mt0) REVERT: A 311 CYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8309 (m) REVERT: A 475 TYR cc_start: 0.7450 (OUTLIER) cc_final: 0.7047 (p90) REVERT: A 620 MET cc_start: 0.7177 (tpt) cc_final: 0.6923 (mmt) REVERT: A 663 TRP cc_start: 0.7526 (OUTLIER) cc_final: 0.6775 (m-10) REVERT: A 664 TRP cc_start: 0.7986 (OUTLIER) cc_final: 0.6687 (p-90) REVERT: A 713 ILE cc_start: 0.4018 (OUTLIER) cc_final: 0.3545 (tp) REVERT: A 716 LEU cc_start: 0.0516 (OUTLIER) cc_final: 0.0066 (pp) REVERT: A 722 ILE cc_start: 0.5114 (OUTLIER) cc_final: 0.4714 (tp) REVERT: A 777 TYR cc_start: 0.4167 (OUTLIER) cc_final: 0.3484 (t80) REVERT: A 1308 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7327 (mm) REVERT: A 1451 TYR cc_start: 0.7517 (OUTLIER) cc_final: 0.6645 (t80) REVERT: A 1562 MET cc_start: 0.3687 (OUTLIER) cc_final: 0.3470 (tmt) REVERT: A 1571 TYR cc_start: 0.7812 (OUTLIER) cc_final: 0.7223 (m-80) REVERT: A 1589 LYS cc_start: 0.2956 (tppt) cc_final: 0.2547 (tppt) REVERT: A 1597 ASN cc_start: 0.8576 (t0) cc_final: 0.8068 (t0) REVERT: A 1603 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7709 (tt) REVERT: A 1770 MET cc_start: 0.6952 (mpp) cc_final: 0.5943 (tpt) outliers start: 47 outliers final: 26 residues processed: 152 average time/residue: 0.1221 time to fit residues: 26.5871 Evaluate side-chains 150 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1192 HIS Chi-restraints excluded: chain A residue 1204 MET Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1451 TYR Chi-restraints excluded: chain A residue 1562 MET Chi-restraints excluded: chain A residue 1571 TYR Chi-restraints excluded: chain A residue 1586 THR Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1689 CYS Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1694 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 83 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 131 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 HIS ** 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 = 0.4424 r_free = 0.4424 target = 0.216878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.170491 restraints weight = 13317.664| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 3.71 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12239 Z= 0.181 Angle : 0.610 10.652 16620 Z= 0.318 Chirality : 0.042 0.175 1845 Planarity : 0.004 0.052 2087 Dihedral : 4.477 57.093 1632 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.61 % Allowed : 24.54 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.23), residues: 1471 helix: 1.50 (0.18), residues: 862 sheet: -0.63 (0.92), residues: 34 loop : -1.58 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 376 TYR 0.019 0.002 TYR A1276 PHE 0.025 0.001 PHE A 517 TRP 0.010 0.001 TRP A1354 HIS 0.004 0.001 HIS A1323 Details of bonding type rmsd covalent geometry : bond 0.00402 (12238) covalent geometry : angle 0.61025 (16618) SS BOND : bond 0.00164 ( 1) SS BOND : angle 0.35436 ( 2) hydrogen bonds : bond 0.08362 ( 641) hydrogen bonds : angle 4.47119 ( 1896) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2942 Ramachandran restraints generated. 1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2942 Ramachandran restraints generated. 1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 110 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 156 GLN cc_start: 0.7946 (mm110) cc_final: 0.7675 (mt0) REVERT: A 311 CYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7996 (m) REVERT: A 475 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.6970 (p90) REVERT: A 620 MET cc_start: 0.6820 (tpt) cc_final: 0.6552 (mmt) REVERT: A 663 TRP cc_start: 0.7577 (OUTLIER) cc_final: 0.6741 (m-10) REVERT: A 713 ILE cc_start: 0.4152 (OUTLIER) cc_final: 0.3817 (tp) REVERT: A 716 LEU cc_start: 0.1429 (OUTLIER) cc_final: 0.0739 (pp) REVERT: A 722 ILE cc_start: 0.5065 (OUTLIER) cc_final: 0.4792 (tp) REVERT: A 777 TYR cc_start: 0.4893 (OUTLIER) cc_final: 0.4184 (t80) REVERT: A 1308 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.6887 (mm) REVERT: A 1496 TRP cc_start: 0.5565 (OUTLIER) cc_final: 0.4999 (m-10) REVERT: A 1562 MET cc_start: 0.3919 (OUTLIER) cc_final: 0.3609 (tmt) REVERT: A 1571 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.7311 (m-80) REVERT: A 1589 LYS cc_start: 0.3230 (tppt) cc_final: 0.2890 (tppt) REVERT: A 1597 ASN cc_start: 0.8182 (t0) cc_final: 0.7945 (t0) REVERT: A 1603 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7683 (tt) REVERT: A 1749 VAL cc_start: 0.8303 (t) cc_final: 0.8086 (t) REVERT: A 1770 MET cc_start: 0.6085 (mpp) cc_final: 0.5634 (tpt) outliers start: 45 outliers final: 27 residues processed: 149 average time/residue: 0.1191 time to fit residues: 25.6412 Evaluate side-chains 150 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1204 MET Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1496 TRP Chi-restraints excluded: chain A residue 1562 MET Chi-restraints excluded: chain A residue 1571 TYR Chi-restraints excluded: chain A residue 1586 THR Chi-restraints excluded: chain A residue 1600 LEU Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1689 CYS Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1694 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 88 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 87 optimal weight: 0.0670 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 138 optimal weight: 0.0170 chunk 2 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.222481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.169289 restraints weight = 13333.858| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 1.72 r_work: 0.3624 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12239 Z= 0.126 Angle : 0.548 10.883 16620 Z= 0.282 Chirality : 0.039 0.169 1845 Planarity : 0.004 0.050 2087 Dihedral : 4.242 57.385 1632 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.97 % Allowed : 25.26 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.23), residues: 1471 helix: 1.80 (0.18), residues: 858 sheet: -0.51 (0.93), residues: 34 loop : -1.56 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1684 TYR 0.011 0.001 TYR A1800 PHE 0.022 0.001 PHE A 238 TRP 0.012 0.001 TRP A 456 HIS 0.004 0.000 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00246 (12238) covalent geometry : angle 0.54809 (16618) SS BOND : bond 0.00054 ( 1) SS BOND : angle 0.55901 ( 2) hydrogen bonds : bond 0.06270 ( 641) hydrogen bonds : angle 4.25412 ( 1896) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2942 Ramachandran restraints generated. 1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2942 Ramachandran restraints generated. 1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 156 GLN cc_start: 0.8107 (mm110) cc_final: 0.7616 (mt0) REVERT: A 475 TYR cc_start: 0.7420 (OUTLIER) cc_final: 0.7000 (p90) REVERT: A 620 MET cc_start: 0.7052 (tpt) cc_final: 0.6685 (mmt) REVERT: A 663 TRP cc_start: 0.7436 (OUTLIER) cc_final: 0.6660 (m-10) REVERT: A 664 TRP cc_start: 0.8116 (OUTLIER) cc_final: 0.6958 (p-90) REVERT: A 713 ILE cc_start: 0.3986 (OUTLIER) cc_final: 0.3480 (tp) REVERT: A 716 LEU cc_start: 0.0567 (OUTLIER) cc_final: 0.0170 (pp) REVERT: A 722 ILE cc_start: 0.5009 (OUTLIER) cc_final: 0.4602 (tp) REVERT: A 777 TYR cc_start: 0.3616 (OUTLIER) cc_final: 0.2748 (t80) REVERT: A 1058 ILE cc_start: 0.7058 (mm) cc_final: 0.6504 (mm) REVERT: A 1204 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.9047 (mmm) REVERT: A 1308 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7234 (mm) REVERT: A 1451 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.6648 (t80) REVERT: A 1562 MET cc_start: 0.3494 (OUTLIER) cc_final: 0.3238 (tmt) REVERT: A 1571 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.7199 (m-80) REVERT: A 1589 LYS cc_start: 0.2974 (tppt) cc_final: 0.2500 (tppt) REVERT: A 1597 ASN cc_start: 0.8433 (t0) cc_final: 0.8149 (t0) REVERT: A 1603 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7667 (tt) REVERT: A 1770 MET cc_start: 0.6793 (mpp) cc_final: 0.5847 (tpt) outliers start: 37 outliers final: 22 residues processed: 145 average time/residue: 0.1190 time to fit residues: 24.8046 Evaluate side-chains 148 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 777 TYR Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1204 MET Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1451 TYR Chi-restraints excluded: chain A residue 1562 MET Chi-restraints excluded: chain A residue 1571 TYR Chi-restraints excluded: chain A residue 1586 THR Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1689 CYS Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1694 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 78 optimal weight: 7.9990 chunk 18 optimal weight: 0.0060 chunk 21 optimal weight: 5.9990 chunk 30 optimal weight: 0.0570 chunk 97 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 overall best weight: 0.4514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.224344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.154870 restraints weight = 13152.556| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.99 r_work: 0.3514 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12239 Z= 0.120 Angle : 0.537 10.440 16620 Z= 0.275 Chirality : 0.039 0.175 1845 Planarity : 0.004 0.050 2087 Dihedral : 4.114 58.473 1632 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.89 % Allowed : 25.42 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.23), residues: 1471 helix: 1.93 (0.18), residues: 854 sheet: 0.06 (0.95), residues: 32 loop : -1.56 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 376 TYR 0.011 0.001 TYR A1800 PHE 0.022 0.001 PHE A 238 TRP 0.011 0.001 TRP A 456 HIS 0.003 0.000 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00240 (12238) covalent geometry : angle 0.53652 (16618) SS BOND : bond 0.00151 ( 1) SS BOND : angle 0.50233 ( 2) hydrogen bonds : bond 0.05644 ( 641) hydrogen bonds : angle 4.16141 ( 1896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3496.79 seconds wall clock time: 60 minutes 25.80 seconds (3625.80 seconds total)