Starting phenix.real_space_refine on Wed Aug 5 01:48:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uk9_64231/08_2026/9uk9_64231.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uk9_64231/08_2026/9uk9_64231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uk9_64231/08_2026/9uk9_64231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uk9_64231/08_2026/9uk9_64231.map" model { file = "/net/cci-nas-00/data/ceres_data/9uk9_64231/08_2026/9uk9_64231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uk9_64231/08_2026/9uk9_64231.cif" } resolution = 3.49 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Co 2 6.85 5 S 25 5.16 5 C 4953 2.51 5 N 1395 2.21 5 O 1462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7837 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7835 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 69, 'TRANS': 953} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.75, per 1000 atoms: 0.22 Number of scatterers: 7837 At special positions: 0 Unit cell: (90.74, 86.552, 106.794, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Co 2 26.99 S 25 16.00 O 1462 8.00 N 1395 7.00 C 4953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 401.0 milliseconds 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1870 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 6 sheets defined 53.9% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 186 through 193 removed outlier: 3.874A pdb=" N HIS A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 216 through 230 Processing helix chain 'A' and resid 243 through 257 Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.303A pdb=" N ARG A 285 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 286 " --> pdb=" O ASP A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 357 through 374 removed outlier: 3.957A pdb=" N VAL A 361 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 417 removed outlier: 3.621A pdb=" N ALA A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 436 removed outlier: 3.654A pdb=" N ALA A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 464 removed outlier: 3.584A pdb=" N LYS A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 478 removed outlier: 3.676A pdb=" N ARG A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP A 477 " --> pdb=" O VAL A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 541 removed outlier: 4.362A pdb=" N LEU A 539 " --> pdb=" O TYR A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 578 Processing helix chain 'A' and resid 590 through 601 removed outlier: 3.971A pdb=" N GLY A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 597 " --> pdb=" O GLU A 593 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A 599 " --> pdb=" O THR A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.702A pdb=" N GLU A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 658 removed outlier: 4.211A pdb=" N ARG A 655 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP A 656 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 664 removed outlier: 3.967A pdb=" N GLY A 664 " --> pdb=" O ASP A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 688 removed outlier: 3.831A pdb=" N LEU A 675 " --> pdb=" O GLU A 671 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 716 removed outlier: 4.147A pdb=" N VAL A 716 " --> pdb=" O ALA A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 731 Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 763 through 767 Processing helix chain 'A' and resid 776 through 790 removed outlier: 4.216A pdb=" N THR A 780 " --> pdb=" O ILE A 776 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL A 781 " --> pdb=" O ALA A 777 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 787 " --> pdb=" O ARG A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 815 removed outlier: 3.594A pdb=" N ALA A 807 " --> pdb=" O THR A 803 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 808 " --> pdb=" O GLN A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 835 removed outlier: 4.175A pdb=" N GLY A 824 " --> pdb=" O VAL A 820 " (cutoff:3.500A) Proline residue: A 825 - end of helix removed outlier: 3.690A pdb=" N LEU A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 833 " --> pdb=" O ASP A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 851 removed outlier: 3.933A pdb=" N GLY A 851 " --> pdb=" O PRO A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 892 removed outlier: 4.180A pdb=" N GLU A 884 " --> pdb=" O LYS A 880 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU A 885 " --> pdb=" O LYS A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 914 removed outlier: 3.605A pdb=" N ARG A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 925 removed outlier: 3.654A pdb=" N ALA A 921 " --> pdb=" O ASP A 917 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 925 " --> pdb=" O ALA A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 950 Processing helix chain 'A' and resid 961 through 968 Processing helix chain 'A' and resid 968 through 985 removed outlier: 3.539A pdb=" N PHE A 975 " --> pdb=" O GLN A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1008 Processing helix chain 'A' and resid 1011 through 1020 Processing helix chain 'A' and resid 1034 through 1042 removed outlier: 4.005A pdb=" N LEU A1038 " --> pdb=" O GLY A1034 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A1040 " --> pdb=" O GLN A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1059 removed outlier: 3.625A pdb=" N LEU A1050 " --> pdb=" O GLY A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1079 removed outlier: 3.873A pdb=" N GLU A1077 " --> pdb=" O GLY A1073 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A1078 " --> pdb=" O LEU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1118 removed outlier: 3.916A pdb=" N GLN A1104 " --> pdb=" O ASP A1100 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A1105 " --> pdb=" O ASP A1101 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A1107 " --> pdb=" O TYR A1103 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A1108 " --> pdb=" O GLN A1104 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A1110 " --> pdb=" O GLU A1106 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A1111 " --> pdb=" O GLY A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1148 removed outlier: 3.886A pdb=" N ARG A1148 " --> pdb=" O SER A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1162 removed outlier: 3.891A pdb=" N ARG A1162 " --> pdb=" O ALA A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1185 removed outlier: 4.715A pdb=" N ILE A1171 " --> pdb=" O GLY A1167 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A1175 " --> pdb=" O ILE A1171 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A1184 " --> pdb=" O ALA A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1201 removed outlier: 3.666A pdb=" N PHE A1193 " --> pdb=" O GLY A1189 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A1195 " --> pdb=" O HIS A1191 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A1196 " --> pdb=" O HIS A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1214 Processing helix chain 'A' and resid 1214 through 1231 removed outlier: 3.545A pdb=" N LEU A1218 " --> pdb=" O ASN A1214 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A1219 " --> pdb=" O PRO A1215 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A1228 " --> pdb=" O LYS A1224 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A1229 " --> pdb=" O LEU A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1255 removed outlier: 4.213A pdb=" N ARG A1242 " --> pdb=" O SER A1238 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE A1243 " --> pdb=" O ASN A1239 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A1246 " --> pdb=" O ARG A1242 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A1247 " --> pdb=" O PHE A1243 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A1252 " --> pdb=" O LEU A1248 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN A1253 " --> pdb=" O SER A1249 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 182 through 185 removed outlier: 4.492A pdb=" N ALA A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N TRP A 179 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A 177 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TRP A 178 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA A 202 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE A 236 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE A 204 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL A 238 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU A 206 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 504 through 507 removed outlier: 6.264A pdb=" N VAL A 548 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N HIS A 550 " --> pdb=" O PRO A 585 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ILE A 587 " --> pdb=" O HIS A 550 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 486 through 487 Processing sheet with id=AA4, first strand: chain 'A' and resid 613 through 615 Processing sheet with id=AA5, first strand: chain 'A' and resid 1060 through 1062 removed outlier: 4.072A pdb=" N VAL A1023 " --> pdb=" O TYR A1062 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N PHE A1024 " --> pdb=" O VAL A 956 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU A 958 " --> pdb=" O PHE A1024 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N SER A 900 " --> pdb=" O ALA A1084 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N VAL A1086 " --> pdb=" O SER A 900 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY A 902 " --> pdb=" O VAL A1086 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ASN A1088 " --> pdb=" O GLY A 902 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N THR A 904 " --> pdb=" O ASN A1088 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL A1085 " --> pdb=" O TYR A1124 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ASN A1126 " --> pdb=" O VAL A1085 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN A1087 " --> pdb=" O ASN A1126 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG A1137 " --> pdb=" O HIS A1125 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A1135 " --> pdb=" O ASP A1127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 927 through 932 removed outlier: 4.133A pdb=" N VAL A 930 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLY A 940 " --> pdb=" O VAL A 930 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP A 932 " --> pdb=" O VAL A 938 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL A 938 " --> pdb=" O ASP A 932 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 1005 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: 1.16 Time building geometry restraints manager: 0.81 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: 2680 1.34 - 1.46: 1589 1.46 - 1.58: 3705 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 8018 Sorted by residual: bond pdb=" N ASP A 854 " pdb=" CA ASP A 854 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.10e-02 8.26e+03 9.07e+00 bond pdb=" CA PRO A 873 " pdb=" CB PRO A 873 " ideal model delta sigma weight residual 1.533 1.492 0.041 1.42e-02 4.96e+03 8.40e+00 bond pdb=" N PRO A 857 " pdb=" CA PRO A 857 " ideal model delta sigma weight residual 1.469 1.506 -0.037 1.28e-02 6.10e+03 8.37e+00 bond pdb=" N VAL A 855 " pdb=" CA VAL A 855 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.71e+00 bond pdb=" N ARG A 852 " pdb=" CA ARG A 852 " ideal model delta sigma weight residual 1.463 1.488 -0.025 9.30e-03 1.16e+04 7.50e+00 ... (remaining 8013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 10638 2.06 - 4.13: 230 4.13 - 6.19: 44 6.19 - 8.26: 4 8.26 - 10.32: 1 Bond angle restraints: 10917 Sorted by residual: angle pdb=" N VAL A 870 " pdb=" CA VAL A 870 " pdb=" CB VAL A 870 " ideal model delta sigma weight residual 111.21 103.40 7.81 1.40e+00 5.10e-01 3.11e+01 angle pdb=" CA HIS A 554 " pdb=" CB HIS A 554 " pdb=" CG HIS A 554 " ideal model delta sigma weight residual 113.80 119.16 -5.36 1.00e+00 1.00e+00 2.88e+01 angle pdb=" C LYS A 553 " pdb=" N HIS A 554 " pdb=" CA HIS A 554 " ideal model delta sigma weight residual 121.87 114.50 7.37 1.64e+00 3.72e-01 2.02e+01 angle pdb=" CA GLY A 552 " pdb=" C GLY A 552 " pdb=" O GLY A 552 " ideal model delta sigma weight residual 121.76 117.95 3.81 8.70e-01 1.32e+00 1.92e+01 angle pdb=" CA PRO A 871 " pdb=" N PRO A 871 " pdb=" CD PRO A 871 " ideal model delta sigma weight residual 112.00 105.89 6.11 1.40e+00 5.10e-01 1.90e+01 ... (remaining 10912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4124 17.82 - 35.64: 508 35.64 - 53.45: 148 53.45 - 71.27: 26 71.27 - 89.09: 8 Dihedral angle restraints: 4814 sinusoidal: 1893 harmonic: 2921 Sorted by residual: dihedral pdb=" C LYS A 553 " pdb=" N LYS A 553 " pdb=" CA LYS A 553 " pdb=" CB LYS A 553 " ideal model delta harmonic sigma weight residual -122.60 -113.27 -9.33 0 2.50e+00 1.60e-01 1.39e+01 dihedral pdb=" C PHE A 586 " pdb=" N PHE A 586 " pdb=" CA PHE A 586 " pdb=" CB PHE A 586 " ideal model delta harmonic sigma weight residual -122.60 -113.72 -8.88 0 2.50e+00 1.60e-01 1.26e+01 dihedral pdb=" CA ASN A 556 " pdb=" CB ASN A 556 " pdb=" CG ASN A 556 " pdb=" OD1 ASN A 556 " ideal model delta sinusoidal sigma weight residual 120.00 -166.26 -73.74 2 2.00e+01 2.50e-03 1.11e+01 ... (remaining 4811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1052 0.067 - 0.133: 126 0.133 - 0.200: 6 0.200 - 0.267: 5 0.267 - 0.333: 3 Chirality restraints: 1192 Sorted by residual: chirality pdb=" CA VAL A 855 " pdb=" N VAL A 855 " pdb=" C VAL A 855 " pdb=" CB VAL A 855 " both_signs ideal model delta sigma weight residual False 2.44 2.77 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA LYS A 553 " pdb=" N LYS A 553 " pdb=" C LYS A 553 " pdb=" CB LYS A 553 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA VAL A 870 " pdb=" N VAL A 870 " pdb=" C VAL A 870 " pdb=" CB VAL A 870 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 1189 not shown) Planarity restraints: 1458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A1133 " 0.057 5.00e-02 4.00e+02 8.46e-02 1.14e+01 pdb=" N PRO A1134 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO A1134 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A1134 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 590 " -0.054 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO A 591 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 591 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 591 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 257 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO A 258 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " -0.040 5.00e-02 4.00e+02 ... (remaining 1455 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1513 2.77 - 3.30: 7759 3.30 - 3.83: 13688 3.83 - 4.37: 15800 4.37 - 4.90: 26158 Nonbonded interactions: 64918 Sorted by model distance: nonbonded pdb=" NH1 ARG A 229 " pdb=" OE1 GLU A 363 " model vdw 2.233 3.120 nonbonded pdb=" OD1 ASP A 740 " pdb=" NE2 GLN A 804 " model vdw 2.236 3.120 nonbonded pdb=" O ALA A 923 " pdb=" NH2 ARG A 951 " model vdw 2.241 3.120 nonbonded pdb=" O SER A1026 " pdb=" OH TYR A1062 " model vdw 2.256 3.040 nonbonded pdb=" NH2 ARG A 444 " pdb=" O PHE A 486 " model vdw 2.273 3.120 ... (remaining 64913 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: 2.350 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.230 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 8018 Z= 0.228 Angle : 0.693 10.321 10917 Z= 0.395 Chirality : 0.047 0.333 1192 Planarity : 0.007 0.090 1458 Dihedral : 17.346 89.088 2944 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.79 % Allowed : 5.30 % Favored : 93.92 % Rotamer: Outliers : 2.02 % Allowed : 27.56 % Favored : 70.42 % 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 are not related in a simple way. whole: -0.43 (0.26), residues: 1019 helix: 0.42 (0.25), residues: 450 sheet: 1.34 (0.57), residues: 86 loop : -1.27 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.000 ARG A 229 TYR 0.012 0.001 TYR A 419 PHE 0.019 0.002 PHE A 862 TRP 0.010 0.001 TRP A1054 HIS 0.005 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.23 ( 8018) covalent geometry : angle 0.69323 / 0.39 (10917) hydrogen bonds : bond 0.25597 / 17.29 ( 344) hydrogen bonds : angle 7.53744 / 5.40 ( 1005) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 854 ASP cc_start: 0.6528 (OUTLIER) cc_final: 0.6094 (m-30) outliers start: 16 outliers final: 11 residues processed: 148 average time/residue: 0.0870 time to fit residues: 17.6082 Evaluate side-chains 150 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 596 GLN Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 871 PRO Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 873 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 530 HIS ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 910 ASN A1083 GLN ** A1094 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.180327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.160107 restraints weight = 12447.142| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.95 r_work: 0.3908 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8018 Z= 0.169 Angle : 0.591 6.855 10917 Z= 0.309 Chirality : 0.043 0.185 1192 Planarity : 0.007 0.069 1458 Dihedral : 6.418 55.204 1150 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.42 % Allowed : 25.03 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.26), residues: 1019 helix: 0.44 (0.23), residues: 486 sheet: 1.27 (0.59), residues: 84 loop : -1.48 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.015 0.002 TYR A 419 PHE 0.028 0.002 PHE A 862 TRP 0.013 0.001 TRP A 897 HIS 0.006 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 8018) covalent geometry : angle 0.59098 / 0.31 (10917) hydrogen bonds : bond 0.04763 / 3.28 ( 344) hydrogen bonds : angle 5.32544 / 3.81 ( 1005) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 782 GLU cc_start: 0.5074 (OUTLIER) cc_final: 0.2062 (pp20) REVERT: A 868 ARG cc_start: 0.7252 (mtt180) cc_final: 0.6989 (mtt180) outliers start: 35 outliers final: 13 residues processed: 165 average time/residue: 0.0884 time to fit residues: 19.5847 Evaluate side-chains 154 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 470 GLN A 556 ASN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1094 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.180303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.160037 restraints weight = 12390.998| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.94 r_work: 0.3927 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8018 Z= 0.157 Angle : 0.558 6.126 10917 Z= 0.291 Chirality : 0.043 0.158 1192 Planarity : 0.007 0.071 1458 Dihedral : 5.755 57.977 1135 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.30 % Allowed : 25.03 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % 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 are not related in a simple way. whole: -0.42 (0.26), residues: 1019 helix: 0.57 (0.23), residues: 484 sheet: 1.16 (0.58), residues: 84 loop : -1.51 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 889 TYR 0.012 0.001 TYR A1103 PHE 0.029 0.002 PHE A 862 TRP 0.016 0.001 TRP A 897 HIS 0.005 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 8018) covalent geometry : angle 0.55844 / 0.29 (10917) hydrogen bonds : bond 0.04276 / 2.94 ( 344) hydrogen bonds : angle 4.97634 / 3.58 ( 1005) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.6766 (m-30) cc_final: 0.6361 (m-30) REVERT: A 414 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6070 (tpp) REVERT: A 782 GLU cc_start: 0.5079 (OUTLIER) cc_final: 0.2708 (tt0) REVERT: A 868 ARG cc_start: 0.7303 (mtt180) cc_final: 0.7036 (mtt180) REVERT: A 1093 GLU cc_start: 0.7447 (mp0) cc_final: 0.6998 (mm-30) REVERT: A 1096 LEU cc_start: 0.8490 (pt) cc_final: 0.8265 (pp) outliers start: 34 outliers final: 19 residues processed: 163 average time/residue: 0.0823 time to fit residues: 18.3714 Evaluate side-chains 159 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 774 TRP Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 862 PHE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1109 MET Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1174 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 83 optimal weight: 0.3980 chunk 86 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 470 GLN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1094 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.182477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.161810 restraints weight = 12600.846| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 3.07 r_work: 0.3947 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8018 Z= 0.133 Angle : 0.539 5.299 10917 Z= 0.279 Chirality : 0.042 0.162 1192 Planarity : 0.006 0.068 1458 Dihedral : 5.002 48.903 1131 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.68 % Allowed : 25.92 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % 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 are not related in a simple way. whole: -0.28 (0.26), residues: 1019 helix: 0.75 (0.23), residues: 484 sheet: 1.05 (0.58), residues: 84 loop : -1.49 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 394 TYR 0.014 0.001 TYR A1103 PHE 0.026 0.002 PHE A 862 TRP 0.014 0.001 TRP A 897 HIS 0.004 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 8018) covalent geometry : angle 0.53857 / 0.28 (10917) hydrogen bonds : bond 0.03669 / 2.52 ( 344) hydrogen bonds : angle 4.84755 / 3.47 ( 1005) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.6790 (m-30) cc_final: 0.6364 (m-30) REVERT: A 392 ASP cc_start: 0.8399 (m-30) cc_final: 0.8002 (m-30) REVERT: A 470 GLN cc_start: 0.7390 (tp-100) cc_final: 0.7178 (tp-100) REVERT: A 782 GLU cc_start: 0.4979 (OUTLIER) cc_final: 0.2979 (tt0) REVERT: A 783 ARG cc_start: 0.6253 (OUTLIER) cc_final: 0.6052 (mtp85) REVERT: A 868 ARG cc_start: 0.7325 (mtt180) cc_final: 0.7103 (mtt180) REVERT: A 1093 GLU cc_start: 0.7401 (mp0) cc_final: 0.6974 (mm-30) REVERT: A 1096 LEU cc_start: 0.8470 (pt) cc_final: 0.8188 (pp) outliers start: 37 outliers final: 22 residues processed: 164 average time/residue: 0.0853 time to fit residues: 19.3631 Evaluate side-chains 162 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 774 TRP Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain A residue 783 ARG Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1109 MET Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1251 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 76 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1094 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 = 0.4292 r_free = 0.4292 target = 0.179662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.158612 restraints weight = 12756.370| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 3.06 r_work: 0.3908 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8018 Z= 0.216 Angle : 0.603 6.277 10917 Z= 0.315 Chirality : 0.044 0.167 1192 Planarity : 0.007 0.070 1458 Dihedral : 4.881 39.866 1131 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.17 % Allowed : 26.17 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % 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 are not related in a simple way. whole: -0.39 (0.26), residues: 1019 helix: 0.65 (0.23), residues: 480 sheet: 1.02 (0.58), residues: 84 loop : -1.53 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1148 TYR 0.013 0.002 TYR A 536 PHE 0.032 0.002 PHE A 862 TRP 0.021 0.002 TRP A 897 HIS 0.007 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 ( 8018) covalent geometry : angle 0.60314 / 0.31 (10917) hydrogen bonds : bond 0.04162 / 2.87 ( 344) hydrogen bonds : angle 4.94171 / 3.52 ( 1005) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.6781 (m-30) cc_final: 0.6331 (m-30) REVERT: A 451 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7469 (mm-30) REVERT: A 470 GLN cc_start: 0.7429 (tp-100) cc_final: 0.7215 (tp-100) REVERT: A 549 VAL cc_start: 0.8210 (t) cc_final: 0.7988 (t) REVERT: A 551 MET cc_start: 0.7722 (mmm) cc_final: 0.7452 (mtm) REVERT: A 626 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7330 (mt-10) REVERT: A 679 ASP cc_start: 0.8228 (t0) cc_final: 0.7992 (t0) REVERT: A 782 GLU cc_start: 0.5332 (OUTLIER) cc_final: 0.3861 (tt0) REVERT: A 832 LEU cc_start: 0.8284 (mt) cc_final: 0.8082 (mm) REVERT: A 868 ARG cc_start: 0.7233 (mtt180) cc_final: 0.7032 (mtt180) REVERT: A 1096 LEU cc_start: 0.8450 (pt) cc_final: 0.8233 (pp) REVERT: A 1171 ILE cc_start: 0.8039 (mm) cc_final: 0.7622 (mt) outliers start: 33 outliers final: 24 residues processed: 168 average time/residue: 0.0754 time to fit residues: 17.7401 Evaluate side-chains 166 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 862 PHE Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1109 MET Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1251 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 9 optimal weight: 3.9990 chunk 23 optimal weight: 0.1980 chunk 87 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 0.0670 chunk 77 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1094 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 = 0.4291 r_free = 0.4291 target = 0.179331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.158515 restraints weight = 12800.158| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 3.04 r_work: 0.3900 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8018 Z= 0.208 Angle : 0.607 6.901 10917 Z= 0.315 Chirality : 0.045 0.167 1192 Planarity : 0.007 0.070 1458 Dihedral : 4.869 39.838 1127 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.80 % Allowed : 26.17 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % 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 are not related in a simple way. whole: -0.47 (0.26), residues: 1019 helix: 0.61 (0.23), residues: 480 sheet: 0.98 (0.57), residues: 84 loop : -1.59 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 379 TYR 0.011 0.002 TYR A 536 PHE 0.032 0.002 PHE A 862 TRP 0.022 0.002 TRP A 897 HIS 0.006 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 ( 8018) covalent geometry : angle 0.60685 / 0.31 (10917) hydrogen bonds : bond 0.04051 / 2.78 ( 344) hydrogen bonds : angle 4.96887 / 3.53 ( 1005) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.6775 (m-30) cc_final: 0.6313 (m-30) REVERT: A 392 ASP cc_start: 0.8424 (m-30) cc_final: 0.8027 (m-30) REVERT: A 414 MET cc_start: 0.7111 (tmm) cc_final: 0.6847 (tmm) REVERT: A 470 GLN cc_start: 0.7484 (tp-100) cc_final: 0.7263 (tp-100) REVERT: A 551 MET cc_start: 0.7744 (mmm) cc_final: 0.7388 (mtm) REVERT: A 679 ASP cc_start: 0.8223 (t0) cc_final: 0.8021 (t0) REVERT: A 782 GLU cc_start: 0.5362 (OUTLIER) cc_final: 0.3056 (tt0) REVERT: A 832 LEU cc_start: 0.8282 (mt) cc_final: 0.8078 (mm) REVERT: A 1093 GLU cc_start: 0.7616 (mp0) cc_final: 0.7110 (mm-30) REVERT: A 1096 LEU cc_start: 0.8460 (pt) cc_final: 0.8196 (pp) REVERT: A 1130 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6623 (mmt90) REVERT: A 1171 ILE cc_start: 0.8058 (mm) cc_final: 0.7640 (mt) REVERT: A 1210 MET cc_start: 0.5370 (mtp) cc_final: 0.5165 (mtp) REVERT: A 1252 LEU cc_start: 0.3409 (OUTLIER) cc_final: 0.3121 (tt) outliers start: 38 outliers final: 28 residues processed: 170 average time/residue: 0.0849 time to fit residues: 19.6024 Evaluate side-chains 167 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 862 PHE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1109 MET Chi-restraints excluded: chain A residue 1130 ARG Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1251 HIS Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 16 optimal weight: 0.0050 chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 0.0170 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 overall best weight: 0.4832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1094 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 = 0.4324 r_free = 0.4324 target = 0.182274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.161374 restraints weight = 12794.441| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 3.07 r_work: 0.3948 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8018 Z= 0.128 Angle : 0.561 5.646 10917 Z= 0.288 Chirality : 0.042 0.164 1192 Planarity : 0.006 0.067 1458 Dihedral : 4.566 37.634 1127 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.55 % Allowed : 27.43 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % 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 are not related in a simple way. whole: -0.24 (0.26), residues: 1019 helix: 0.87 (0.23), residues: 480 sheet: 0.97 (0.58), residues: 84 loop : -1.54 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 379 TYR 0.019 0.001 TYR A1103 PHE 0.026 0.002 PHE A 862 TRP 0.018 0.001 TRP A 897 HIS 0.003 0.001 HIS A1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 8018) covalent geometry : angle 0.56061 / 0.29 (10917) hydrogen bonds : bond 0.03424 / 2.32 ( 344) hydrogen bonds : angle 4.79928 / 3.43 ( 1005) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.6750 (m-30) cc_final: 0.6369 (m-30) REVERT: A 392 ASP cc_start: 0.8316 (m-30) cc_final: 0.7772 (m-30) REVERT: A 448 GLU cc_start: 0.7708 (tm-30) cc_final: 0.6938 (tm-30) REVERT: A 551 MET cc_start: 0.7592 (mmm) cc_final: 0.7243 (mtm) REVERT: A 782 GLU cc_start: 0.5253 (OUTLIER) cc_final: 0.3178 (tt0) REVERT: A 832 LEU cc_start: 0.8138 (mt) cc_final: 0.7926 (mm) REVERT: A 1093 GLU cc_start: 0.7547 (mp0) cc_final: 0.6929 (mm-30) REVERT: A 1096 LEU cc_start: 0.8418 (pt) cc_final: 0.8182 (pp) REVERT: A 1130 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6583 (mmt90) REVERT: A 1252 LEU cc_start: 0.3361 (OUTLIER) cc_final: 0.3082 (tt) outliers start: 36 outliers final: 24 residues processed: 161 average time/residue: 0.0711 time to fit residues: 15.4438 Evaluate side-chains 164 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1109 MET Chi-restraints excluded: chain A residue 1130 ARG Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1251 HIS Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 12 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 40 optimal weight: 0.0050 chunk 49 optimal weight: 0.0370 chunk 86 optimal weight: 4.9990 chunk 73 optimal weight: 0.3980 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.3672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 470 GLN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1094 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.183285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.162563 restraints weight = 12715.284| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 3.06 r_work: 0.3964 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8018 Z= 0.118 Angle : 0.568 10.130 10917 Z= 0.288 Chirality : 0.041 0.171 1192 Planarity : 0.006 0.070 1458 Dihedral : 4.457 36.687 1127 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 4.05 % Allowed : 27.56 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % 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 are not related in a simple way. whole: -0.10 (0.26), residues: 1019 helix: 0.98 (0.23), residues: 485 sheet: 0.97 (0.59), residues: 84 loop : -1.47 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 868 TYR 0.018 0.001 TYR A1103 PHE 0.024 0.001 PHE A 862 TRP 0.014 0.001 TRP A 897 HIS 0.004 0.001 HIS A1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 8018) covalent geometry : angle 0.56823 / 0.29 (10917) hydrogen bonds : bond 0.03205 / 2.15 ( 344) hydrogen bonds : angle 4.71505 / 3.36 ( 1005) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.6610 (m-30) cc_final: 0.6188 (m-30) REVERT: A 392 ASP cc_start: 0.8236 (m-30) cc_final: 0.7763 (m-30) REVERT: A 551 MET cc_start: 0.7604 (mmm) cc_final: 0.7265 (mtm) REVERT: A 782 GLU cc_start: 0.5191 (OUTLIER) cc_final: 0.3049 (tt0) REVERT: A 1093 GLU cc_start: 0.7497 (mp0) cc_final: 0.7056 (mm-30) REVERT: A 1096 LEU cc_start: 0.8407 (pt) cc_final: 0.8137 (pp) REVERT: A 1130 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.6623 (mmt90) REVERT: A 1142 GLU cc_start: 0.7164 (tp30) cc_final: 0.6938 (tp30) REVERT: A 1252 LEU cc_start: 0.3413 (OUTLIER) cc_final: 0.3149 (tt) outliers start: 32 outliers final: 23 residues processed: 158 average time/residue: 0.0767 time to fit residues: 16.4741 Evaluate side-chains 163 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 596 GLN Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1109 MET Chi-restraints excluded: chain A residue 1130 ARG Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1251 HIS Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 0.9980 chunk 49 optimal weight: 0.0870 chunk 6 optimal weight: 10.0000 chunk 73 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 0.0020 chunk 21 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.4366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 470 GLN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1094 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.183615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.163090 restraints weight = 12579.069| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 2.98 r_work: 0.3984 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8018 Z= 0.121 Angle : 0.577 13.525 10917 Z= 0.290 Chirality : 0.042 0.172 1192 Planarity : 0.006 0.066 1458 Dihedral : 4.434 37.288 1127 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.67 % Allowed : 28.45 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % 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 are not related in a simple way. whole: -0.07 (0.26), residues: 1019 helix: 1.00 (0.24), residues: 485 sheet: 1.08 (0.60), residues: 83 loop : -1.48 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1148 TYR 0.018 0.001 TYR A1103 PHE 0.023 0.001 PHE A 862 TRP 0.015 0.001 TRP A 897 HIS 0.004 0.001 HIS A1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 8018) covalent geometry : angle 0.57739 / 0.29 (10917) hydrogen bonds : bond 0.03158 / 2.14 ( 344) hydrogen bonds : angle 4.66783 / 3.32 ( 1005) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.6618 (m-30) cc_final: 0.6238 (m-30) REVERT: A 551 MET cc_start: 0.7563 (mmm) cc_final: 0.7192 (mtm) REVERT: A 754 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7425 (mmm) REVERT: A 782 GLU cc_start: 0.5163 (OUTLIER) cc_final: 0.3119 (tt0) REVERT: A 1093 GLU cc_start: 0.7464 (mp0) cc_final: 0.7009 (mm-30) REVERT: A 1096 LEU cc_start: 0.8395 (pt) cc_final: 0.8165 (pp) REVERT: A 1130 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.6572 (mmt90) REVERT: A 1230 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7150 (tm-30) REVERT: A 1252 LEU cc_start: 0.3454 (OUTLIER) cc_final: 0.3200 (tt) outliers start: 29 outliers final: 20 residues processed: 151 average time/residue: 0.0703 time to fit residues: 14.3464 Evaluate side-chains 159 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1109 MET Chi-restraints excluded: chain A residue 1130 ARG Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1251 HIS Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 56 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 397 ASN A 470 GLN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1094 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.184354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.163845 restraints weight = 12534.255| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 2.97 r_work: 0.3987 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8018 Z= 0.119 Angle : 0.577 12.214 10917 Z= 0.289 Chirality : 0.041 0.176 1192 Planarity : 0.006 0.065 1458 Dihedral : 4.404 37.452 1127 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.67 % Allowed : 28.45 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % 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 are not related in a simple way. whole: -0.01 (0.26), residues: 1019 helix: 1.07 (0.24), residues: 485 sheet: 0.98 (0.60), residues: 85 loop : -1.44 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 379 TYR 0.019 0.001 TYR A1103 PHE 0.023 0.001 PHE A 862 TRP 0.014 0.001 TRP A 897 HIS 0.003 0.001 HIS A1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 8018) covalent geometry : angle 0.57688 / 0.29 (10917) hydrogen bonds : bond 0.03071 / 2.07 ( 344) hydrogen bonds : angle 4.62795 / 3.29 ( 1005) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.6563 (m-30) cc_final: 0.6187 (m-30) REVERT: A 551 MET cc_start: 0.7515 (mmm) cc_final: 0.7167 (mtm) REVERT: A 754 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7484 (mmm) REVERT: A 782 GLU cc_start: 0.5155 (OUTLIER) cc_final: 0.3110 (tt0) REVERT: A 933 MET cc_start: 0.7096 (mmm) cc_final: 0.6703 (mmm) REVERT: A 948 LYS cc_start: 0.8733 (ttpt) cc_final: 0.8435 (ttpp) REVERT: A 1093 GLU cc_start: 0.7405 (mp0) cc_final: 0.7013 (mm-30) REVERT: A 1096 LEU cc_start: 0.8396 (pt) cc_final: 0.8119 (pp) REVERT: A 1114 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6850 (mm-30) REVERT: A 1130 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6627 (mmt90) REVERT: A 1230 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7102 (tm-30) REVERT: A 1252 LEU cc_start: 0.3475 (OUTLIER) cc_final: 0.3218 (tt) outliers start: 29 outliers final: 21 residues processed: 152 average time/residue: 0.0753 time to fit residues: 15.8188 Evaluate side-chains 159 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1109 MET Chi-restraints excluded: chain A residue 1130 ARG Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1251 HIS Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 58 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 397 ASN A 470 GLN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1094 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.184118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.163586 restraints weight = 12610.001| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 3.00 r_work: 0.3989 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8018 Z= 0.125 Angle : 0.578 11.903 10917 Z= 0.290 Chirality : 0.042 0.183 1192 Planarity : 0.006 0.064 1458 Dihedral : 4.419 37.888 1127 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.41 % Allowed : 28.57 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % 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 are not related in a simple way. whole: 0.01 (0.27), residues: 1019 helix: 1.10 (0.24), residues: 485 sheet: 0.91 (0.61), residues: 85 loop : -1.43 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 379 TYR 0.016 0.001 TYR A1103 PHE 0.024 0.002 PHE A 862 TRP 0.016 0.001 TRP A 897 HIS 0.003 0.001 HIS A1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 8018) covalent geometry : angle 0.57774 / 0.29 (10917) hydrogen bonds : bond 0.03085 / 2.09 ( 344) hydrogen bonds : angle 4.62112 / 3.28 ( 1005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1447.44 seconds wall clock time: 25 minutes 38.15 seconds (1538.15 seconds total)