Starting phenix.real_space_refine on Thu Feb 13 20:56:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8woi_37690/02_2025/8woi_37690.cif Found real_map, /net/cci-nas-00/data/ceres_data/8woi_37690/02_2025/8woi_37690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8woi_37690/02_2025/8woi_37690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8woi_37690/02_2025/8woi_37690.map" model { file = "/net/cci-nas-00/data/ceres_data/8woi_37690/02_2025/8woi_37690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8woi_37690/02_2025/8woi_37690.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.100 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 38 5.16 5 C 5965 2.51 5 N 1587 2.21 5 O 1734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9324 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1217, 9324 Classifications: {'peptide': 1217} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 30, 'TRANS': 1186} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 5.61, per 1000 atoms: 0.60 Number of scatterers: 9324 At special positions: 0 Unit cell: (72.6, 106.7, 144.1, 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 38 16.00 O 1734 8.00 N 1587 7.00 C 5965 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: 2.27 Conformation dependent library (CDL) restraints added in 1.3 seconds 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 7 sheets defined 47.7% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 39 through 53 removed outlier: 3.564A pdb=" N VAL A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER A 45 " --> pdb=" O MET A 41 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 67 removed outlier: 3.546A pdb=" N PHE A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 Processing helix chain 'A' and resid 88 through 99 Processing helix chain 'A' and resid 112 through 117 removed outlier: 3.917A pdb=" N VAL A 116 " --> pdb=" O GLY A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.664A pdb=" N GLU A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 150 through 160 removed outlier: 3.564A pdb=" N VAL A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 176 removed outlier: 3.689A pdb=" N TYR A 169 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 184 removed outlier: 3.524A pdb=" N VAL A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 184 " --> pdb=" O GLY A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 178 through 184' Processing helix chain 'A' and resid 186 through 191 removed outlier: 3.766A pdb=" N LEU A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 200 Processing helix chain 'A' and resid 204 through 221 removed outlier: 4.174A pdb=" N THR A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.500A pdb=" N ILE A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 254 through 263 removed outlier: 4.094A pdb=" N LYS A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 273 removed outlier: 4.102A pdb=" N GLY A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 281 Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.585A pdb=" N VAL A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 302 through 311 removed outlier: 3.575A pdb=" N THR A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.656A pdb=" N ASN A 324 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 325 " --> pdb=" O PHE A 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 321 through 325' Processing helix chain 'A' and resid 326 through 342 removed outlier: 3.639A pdb=" N LYS A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 434 removed outlier: 3.874A pdb=" N LEU A 434 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 470 through 479 removed outlier: 3.717A pdb=" N GLU A 474 " --> pdb=" O MET A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 520 removed outlier: 3.740A pdb=" N MET A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 547 removed outlier: 3.548A pdb=" N ILE A 541 " --> pdb=" O SER A 537 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 565 removed outlier: 3.699A pdb=" N THR A 564 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 605 Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.591A pdb=" N HIS A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 666 removed outlier: 3.641A pdb=" N THR A 666 " --> pdb=" O THR A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 680 removed outlier: 3.777A pdb=" N LEU A 677 " --> pdb=" O PHE A 673 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 679 " --> pdb=" O ARG A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 695 removed outlier: 3.703A pdb=" N ILE A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 708 removed outlier: 3.656A pdb=" N THR A 703 " --> pdb=" O PHE A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 715 Processing helix chain 'A' and resid 731 through 737 Processing helix chain 'A' and resid 739 through 744 removed outlier: 3.961A pdb=" N GLY A 743 " --> pdb=" O LEU A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 751 removed outlier: 3.504A pdb=" N HIS A 749 " --> pdb=" O TYR A 745 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 751 " --> pdb=" O ILE A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 772 removed outlier: 3.508A pdb=" N SER A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 770 " --> pdb=" O MET A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 774 No H-bonds generated for 'chain 'A' and resid 773 through 774' Processing helix chain 'A' and resid 775 through 779 Processing helix chain 'A' and resid 800 through 805 removed outlier: 3.691A pdb=" N ILE A 804 " --> pdb=" O VAL A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 821 removed outlier: 3.981A pdb=" N ASN A 814 " --> pdb=" O VAL A 810 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 820 " --> pdb=" O THR A 816 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 829 removed outlier: 3.871A pdb=" N GLU A 829 " --> pdb=" O ALA A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 853 removed outlier: 3.686A pdb=" N LEU A 835 " --> pdb=" O ARG A 831 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 837 " --> pdb=" O SER A 833 " (cutoff:3.500A) Proline residue: A 841 - end of helix removed outlier: 4.050A pdb=" N ALA A 846 " --> pdb=" O LEU A 842 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 865 removed outlier: 4.067A pdb=" N ALA A 864 " --> pdb=" O ASP A 860 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 860 through 865' Processing helix chain 'A' and resid 866 through 873 removed outlier: 3.563A pdb=" N ILE A 871 " --> pdb=" O LYS A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 884 removed outlier: 3.620A pdb=" N ALA A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 892 removed outlier: 3.765A pdb=" N ILE A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A 892 " --> pdb=" O GLN A 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 887 through 892' Processing helix chain 'A' and resid 892 through 897 Processing helix chain 'A' and resid 899 through 921 removed outlier: 3.625A pdb=" N GLN A 903 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 906 " --> pdb=" O PRO A 902 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 912 " --> pdb=" O TYR A 908 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY A 918 " --> pdb=" O GLY A 914 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A 921 " --> pdb=" O PHE A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 926 Processing helix chain 'A' and resid 927 through 939 removed outlier: 3.779A pdb=" N ILE A 931 " --> pdb=" O SER A 927 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 938 " --> pdb=" O TYR A 934 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 939 " --> pdb=" O GLY A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 967 removed outlier: 3.846A pdb=" N VAL A 952 " --> pdb=" O LYS A 948 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN A 961 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER A 962 " --> pdb=" O ILE A 958 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 964 " --> pdb=" O ALA A 960 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU A 965 " --> pdb=" O ASN A 961 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 966 " --> pdb=" O SER A 962 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 975 removed outlier: 3.744A pdb=" N ILE A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1079 No H-bonds generated for 'chain 'A' and resid 1077 through 1079' Processing helix chain 'A' and resid 1084 through 1088 removed outlier: 3.619A pdb=" N ILE A1088 " --> pdb=" O ARG A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1123 Processing helix chain 'A' and resid 1127 through 1133 Processing helix chain 'A' and resid 1150 through 1165 removed outlier: 3.830A pdb=" N GLN A1155 " --> pdb=" O GLY A1151 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG A1156 " --> pdb=" O GLY A1152 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A1157 " --> pdb=" O GLN A1153 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA A1160 " --> pdb=" O ARG A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1194 removed outlier: 3.719A pdb=" N GLU A1192 " --> pdb=" O GLN A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1247 removed outlier: 3.906A pdb=" N LEU A1244 " --> pdb=" O ALA A1240 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 386 through 387 removed outlier: 5.768A pdb=" N PHE A 367 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU A 425 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASP A 369 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN A 423 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 421 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 558 through 559 removed outlier: 6.489A pdb=" N VAL A 398 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL A 573 " --> pdb=" O VAL A 580 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 443 through 445 removed outlier: 6.363A pdb=" N GLY A 444 " --> pdb=" O LEU A 526 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 645 through 647 Processing sheet with id=AA5, first strand: chain 'A' and resid 1028 through 1034 removed outlier: 5.727A pdb=" N ARG A1029 " --> pdb=" O PHE A1017 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N PHE A1017 " --> pdb=" O ARG A1029 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LEU A1033 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ARG A1013 " --> pdb=" O LEU A1033 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1169 through 1171 Processing sheet with id=AA7, first strand: chain 'A' and resid 1217 through 1220 removed outlier: 7.104A pdb=" N VAL A1218 " --> pdb=" O VAL A1225 " (cutoff:3.500A) 251 hydrogen bonds defined for protein. 705 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: 3.16 Time building geometry restraints manager: 2.66 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: 2928 1.34 - 1.45: 1406 1.45 - 1.57: 5096 1.57 - 1.69: 0 1.69 - 1.81: 67 Bond restraints: 9497 Sorted by residual: bond pdb=" CA SER A 631 " pdb=" C SER A 631 " ideal model delta sigma weight residual 1.522 1.460 0.062 1.34e-02 5.57e+03 2.17e+01 bond pdb=" CA TYR A 336 " pdb=" CB TYR A 336 " ideal model delta sigma weight residual 1.530 1.457 0.073 1.63e-02 3.76e+03 2.01e+01 bond pdb=" N LEU A 632 " pdb=" CA LEU A 632 " ideal model delta sigma weight residual 1.453 1.403 0.050 1.37e-02 5.33e+03 1.35e+01 bond pdb=" CA ARG A 635 " pdb=" C ARG A 635 " ideal model delta sigma weight residual 1.522 1.478 0.043 1.25e-02 6.40e+03 1.21e+01 bond pdb=" CA TYR A 336 " pdb=" C TYR A 336 " ideal model delta sigma weight residual 1.524 1.490 0.035 1.29e-02 6.01e+03 7.18e+00 ... (remaining 9492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.26: 12818 7.26 - 14.53: 24 14.53 - 21.79: 4 21.79 - 29.05: 2 29.05 - 36.32: 2 Bond angle restraints: 12850 Sorted by residual: angle pdb=" N ASP A1111 " pdb=" CA ASP A1111 " pdb=" C ASP A1111 " ideal model delta sigma weight residual 109.95 73.63 36.32 1.44e+00 4.82e-01 6.36e+02 angle pdb=" N LYS A1110 " pdb=" CA LYS A1110 " pdb=" C LYS A1110 " ideal model delta sigma weight residual 108.99 76.22 32.77 1.57e+00 4.06e-01 4.36e+02 angle pdb=" N LEU A 632 " pdb=" CA LEU A 632 " pdb=" C LEU A 632 " ideal model delta sigma weight residual 110.41 91.21 19.20 1.23e+00 6.61e-01 2.44e+02 angle pdb=" N ARG A 635 " pdb=" CA ARG A 635 " pdb=" C ARG A 635 " ideal model delta sigma weight residual 114.09 90.77 23.32 1.55e+00 4.16e-01 2.26e+02 angle pdb=" C ASP A1111 " pdb=" CA ASP A1111 " pdb=" CB ASP A1111 " ideal model delta sigma weight residual 111.48 137.08 -25.60 1.91e+00 2.74e-01 1.80e+02 ... (remaining 12845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 5302 15.13 - 30.26: 260 30.26 - 45.39: 67 45.39 - 60.52: 2 60.52 - 75.65: 9 Dihedral angle restraints: 5640 sinusoidal: 2152 harmonic: 3488 Sorted by residual: dihedral pdb=" N ASP A1111 " pdb=" C ASP A1111 " pdb=" CA ASP A1111 " pdb=" CB ASP A1111 " ideal model delta harmonic sigma weight residual 122.80 86.85 35.95 0 2.50e+00 1.60e-01 2.07e+02 dihedral pdb=" C LEU A 634 " pdb=" N LEU A 634 " pdb=" CA LEU A 634 " pdb=" CB LEU A 634 " ideal model delta harmonic sigma weight residual -122.60 -97.48 -25.12 0 2.50e+00 1.60e-01 1.01e+02 dihedral pdb=" N LEU A 634 " pdb=" C LEU A 634 " pdb=" CA LEU A 634 " pdb=" CB LEU A 634 " ideal model delta harmonic sigma weight residual 122.80 97.87 24.93 0 2.50e+00 1.60e-01 9.94e+01 ... (remaining 5637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 1459 0.149 - 0.298: 16 0.298 - 0.447: 1 0.447 - 0.596: 1 0.596 - 0.745: 2 Chirality restraints: 1479 Sorted by residual: chirality pdb=" CA SER A 633 " pdb=" N SER A 633 " pdb=" C SER A 633 " pdb=" CB SER A 633 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" CA LEU A 634 " pdb=" N LEU A 634 " pdb=" C LEU A 634 " pdb=" CB LEU A 634 " both_signs ideal model delta sigma weight residual False 2.51 3.12 -0.61 2.00e-01 2.50e+01 9.42e+00 chirality pdb=" CA LYS A1110 " pdb=" N LYS A1110 " pdb=" C LYS A1110 " pdb=" CB LYS A1110 " both_signs ideal model delta sigma weight residual False 2.51 3.04 -0.52 2.00e-01 2.50e+01 6.89e+00 ... (remaining 1476 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 681 " -0.068 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO A 682 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 682 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 682 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 55 " -0.044 5.00e-02 4.00e+02 6.52e-02 6.79e+00 pdb=" N PRO A 56 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 56 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 56 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 701 " 0.037 5.00e-02 4.00e+02 5.60e-02 5.01e+00 pdb=" N PRO A 702 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 702 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 702 " 0.031 5.00e-02 4.00e+02 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 19 2.43 - 3.05: 5078 3.05 - 3.67: 13044 3.67 - 4.28: 19500 4.28 - 4.90: 32246 Nonbonded interactions: 69887 Sorted by model distance: nonbonded pdb=" N ASP A1111 " pdb=" O ASP A1111 " model vdw 1.818 2.496 nonbonded pdb=" N LYS A1110 " pdb=" O LYS A1110 " model vdw 1.897 2.496 nonbonded pdb=" N ARG A 635 " pdb=" N SER A 636 " model vdw 2.086 2.560 nonbonded pdb=" N LEU A 632 " pdb=" O LEU A 632 " model vdw 2.168 2.496 nonbonded pdb=" OE2 GLU A 829 " pdb=" OG SER A 944 " model vdw 2.291 3.040 ... (remaining 69882 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: 0.940 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.090 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 : 0.005 0.073 9497 Z= 0.307 Angle : 1.204 36.318 12850 Z= 0.719 Chirality : 0.062 0.745 1479 Planarity : 0.007 0.103 1640 Dihedral : 10.494 75.652 3412 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.07 % Favored : 90.85 % Rotamer: Outliers : 0.10 % Allowed : 2.24 % Favored : 97.66 % Cbeta Deviations : 0.54 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.42 (0.16), residues: 1213 helix: -4.82 (0.07), residues: 688 sheet: -2.61 (0.65), residues: 71 loop : -3.22 (0.24), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 933 HIS 0.010 0.002 HIS A 51 PHE 0.026 0.002 PHE A 752 TYR 0.017 0.002 TYR A 110 ARG 0.007 0.001 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.979 Fit side-chains REVERT: A 87 SER cc_start: 0.9082 (p) cc_final: 0.8681 (m) REVERT: A 398 VAL cc_start: 0.9076 (t) cc_final: 0.8860 (p) REVERT: A 604 MET cc_start: 0.7160 (ptm) cc_final: 0.6586 (ttp) REVERT: A 725 ARG cc_start: 0.8087 (ptp90) cc_final: 0.7857 (ptp90) REVERT: A 815 MET cc_start: 0.7582 (mmp) cc_final: 0.7351 (mmp) REVERT: A 1055 ILE cc_start: 0.8741 (pt) cc_final: 0.8305 (mt) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.2921 time to fit residues: 60.6771 Evaluate side-chains 91 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 36 optimal weight: 0.2980 chunk 57 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 168 HIS A 448 GLN ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 GLN A 748 GLN A 758 ASN A 784 HIS A1041 GLN A1205 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.166328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.119968 restraints weight = 11408.987| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.21 r_work: 0.3064 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9497 Z= 0.190 Angle : 0.639 12.019 12850 Z= 0.344 Chirality : 0.042 0.151 1479 Planarity : 0.005 0.083 1640 Dihedral : 6.470 32.834 1323 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 1.53 % Allowed : 7.02 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.15 (0.19), residues: 1213 helix: -3.70 (0.13), residues: 672 sheet: -2.40 (0.64), residues: 71 loop : -2.85 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 933 HIS 0.003 0.001 HIS A 937 PHE 0.027 0.002 PHE A 134 TYR 0.013 0.001 TYR A 262 ARG 0.004 0.000 ARG A1013 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.091 Fit side-chains REVERT: A 39 LEU cc_start: 0.8950 (tt) cc_final: 0.8725 (tp) REVERT: A 270 LEU cc_start: 0.8316 (mt) cc_final: 0.8097 (mt) REVERT: A 339 MET cc_start: 0.8914 (mmm) cc_final: 0.8605 (mmm) REVERT: A 384 ARG cc_start: 0.8551 (ttp80) cc_final: 0.8269 (ptp90) REVERT: A 488 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8700 (mt) REVERT: A 604 MET cc_start: 0.8037 (ptm) cc_final: 0.7423 (ttp) REVERT: A 653 ARG cc_start: 0.5746 (ptp-170) cc_final: 0.5410 (ttp-170) REVERT: A 815 MET cc_start: 0.8463 (mmp) cc_final: 0.8217 (mmp) REVERT: A 904 LYS cc_start: 0.8115 (mttt) cc_final: 0.7766 (ttpp) REVERT: A 1026 MET cc_start: 0.7596 (tpp) cc_final: 0.7390 (tpp) outliers start: 15 outliers final: 5 residues processed: 121 average time/residue: 0.2647 time to fit residues: 43.5806 Evaluate side-chains 91 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 1087 LYS Chi-restraints excluded: chain A residue 1200 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 43 optimal weight: 0.2980 chunk 110 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 5 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 106 optimal weight: 0.2980 chunk 109 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 ASN A1188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.169555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.125353 restraints weight = 11343.010| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.29 r_work: 0.3053 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9497 Z= 0.140 Angle : 0.565 12.787 12850 Z= 0.303 Chirality : 0.040 0.138 1479 Planarity : 0.004 0.071 1640 Dihedral : 5.747 33.021 1323 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 1.02 % Allowed : 8.95 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.21), residues: 1213 helix: -2.92 (0.16), residues: 678 sheet: -1.92 (0.71), residues: 66 loop : -2.62 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 933 HIS 0.002 0.000 HIS A1205 PHE 0.020 0.001 PHE A 134 TYR 0.008 0.001 TYR A1241 ARG 0.004 0.000 ARG A1029 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 1.084 Fit side-chains REVERT: A 39 LEU cc_start: 0.8902 (tt) cc_final: 0.8650 (tp) REVERT: A 384 ARG cc_start: 0.8479 (ttp80) cc_final: 0.8193 (ptp90) REVERT: A 488 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8660 (mt) REVERT: A 548 ARG cc_start: 0.7805 (mtm180) cc_final: 0.7589 (mtm180) REVERT: A 550 MET cc_start: 0.8300 (mtp) cc_final: 0.8049 (mtp) REVERT: A 604 MET cc_start: 0.7931 (ptm) cc_final: 0.7383 (ttm) REVERT: A 653 ARG cc_start: 0.5702 (ptp-170) cc_final: 0.5330 (ttp-170) REVERT: A 708 MET cc_start: 0.9141 (tmm) cc_final: 0.8891 (ttt) REVERT: A 904 LYS cc_start: 0.8076 (mttt) cc_final: 0.7756 (ttpp) REVERT: A 1026 MET cc_start: 0.7560 (tpp) cc_final: 0.7313 (tpp) outliers start: 10 outliers final: 4 residues processed: 102 average time/residue: 0.2574 time to fit residues: 36.2088 Evaluate side-chains 84 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 1087 LYS Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1216 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 0.0070 chunk 88 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** 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 = 0.3864 r_free = 0.3864 target = 0.166460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.120877 restraints weight = 11204.807| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.25 r_work: 0.3090 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9497 Z= 0.182 Angle : 0.566 10.282 12850 Z= 0.303 Chirality : 0.041 0.149 1479 Planarity : 0.004 0.073 1640 Dihedral : 5.569 32.623 1323 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.32 % Allowed : 9.77 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.22), residues: 1213 helix: -2.47 (0.18), residues: 682 sheet: -1.72 (0.72), residues: 64 loop : -2.59 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 933 HIS 0.003 0.000 HIS A 937 PHE 0.018 0.001 PHE A 438 TYR 0.009 0.001 TYR A1062 ARG 0.003 0.000 ARG A1036 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 1.077 Fit side-chains REVERT: A 39 LEU cc_start: 0.8906 (tt) cc_final: 0.8692 (tp) REVERT: A 384 ARG cc_start: 0.8512 (ttp80) cc_final: 0.8201 (ptp90) REVERT: A 488 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8868 (mt) REVERT: A 550 MET cc_start: 0.8222 (mtp) cc_final: 0.7976 (mtp) REVERT: A 604 MET cc_start: 0.7783 (ptm) cc_final: 0.7296 (ttm) REVERT: A 653 ARG cc_start: 0.5753 (ptp-170) cc_final: 0.5470 (ttp-170) REVERT: A 904 LYS cc_start: 0.8257 (mttt) cc_final: 0.8021 (ttpp) REVERT: A 1026 MET cc_start: 0.7674 (tpp) cc_final: 0.7294 (tpp) REVERT: A 1074 LYS cc_start: 0.7507 (mtpp) cc_final: 0.6940 (mtmm) outliers start: 13 outliers final: 6 residues processed: 95 average time/residue: 0.2981 time to fit residues: 38.7153 Evaluate side-chains 87 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 1087 LYS Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1216 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 92 optimal weight: 0.2980 chunk 83 optimal weight: 0.8980 chunk 63 optimal weight: 0.0670 chunk 80 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 117 optimal weight: 9.9990 chunk 79 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** 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 = 0.3910 r_free = 0.3910 target = 0.170704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.125267 restraints weight = 11184.632| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.24 r_work: 0.3075 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9497 Z= 0.130 Angle : 0.518 8.520 12850 Z= 0.278 Chirality : 0.040 0.142 1479 Planarity : 0.003 0.068 1640 Dihedral : 5.193 32.362 1323 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.63 % Allowed : 10.58 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.22), residues: 1213 helix: -2.09 (0.19), residues: 677 sheet: -2.00 (0.67), residues: 67 loop : -2.45 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 933 HIS 0.001 0.000 HIS A1205 PHE 0.020 0.001 PHE A 305 TYR 0.007 0.001 TYR A1241 ARG 0.004 0.000 ARG A1029 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8835 (tt) cc_final: 0.8612 (tp) REVERT: A 74 MET cc_start: 0.8450 (mmp) cc_final: 0.8217 (mmt) REVERT: A 438 PHE cc_start: 0.8557 (t80) cc_final: 0.8119 (t80) REVERT: A 488 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8822 (mt) REVERT: A 544 GLU cc_start: 0.7554 (pp20) cc_final: 0.7063 (tm-30) REVERT: A 548 ARG cc_start: 0.7852 (mtm180) cc_final: 0.6612 (mtt180) REVERT: A 550 MET cc_start: 0.8273 (mtp) cc_final: 0.8034 (mtp) REVERT: A 604 MET cc_start: 0.7797 (ptm) cc_final: 0.7295 (ttm) REVERT: A 653 ARG cc_start: 0.5742 (ptp-170) cc_final: 0.5383 (ttp-170) REVERT: A 656 MET cc_start: 0.8701 (mtt) cc_final: 0.8477 (mtm) REVERT: A 740 TYR cc_start: 0.8685 (t80) cc_final: 0.8461 (t80) REVERT: A 904 LYS cc_start: 0.8076 (mttt) cc_final: 0.7834 (ttpp) REVERT: A 1074 LYS cc_start: 0.7373 (mtpp) cc_final: 0.6866 (mtmm) outliers start: 16 outliers final: 6 residues processed: 101 average time/residue: 0.2627 time to fit residues: 35.7791 Evaluate side-chains 88 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1216 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 49 optimal weight: 0.0470 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 78 optimal weight: 0.4980 chunk 111 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 GLN ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.168835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124775 restraints weight = 11183.142| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.41 r_work: 0.2969 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9497 Z= 0.212 Angle : 0.558 7.465 12850 Z= 0.297 Chirality : 0.042 0.139 1479 Planarity : 0.004 0.069 1640 Dihedral : 5.292 32.922 1323 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 1.02 % Allowed : 11.80 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.23), residues: 1213 helix: -1.99 (0.19), residues: 676 sheet: -2.06 (0.66), residues: 70 loop : -2.39 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 933 HIS 0.003 0.001 HIS A 784 PHE 0.020 0.001 PHE A 69 TYR 0.009 0.001 TYR A 740 ARG 0.005 0.000 ARG A1029 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8898 (tt) cc_final: 0.8663 (tp) REVERT: A 74 MET cc_start: 0.8546 (mmp) cc_final: 0.8317 (mmt) REVERT: A 368 LYS cc_start: 0.7779 (mmmm) cc_final: 0.7512 (mmmm) REVERT: A 488 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8903 (mt) REVERT: A 544 GLU cc_start: 0.7622 (pp20) cc_final: 0.7216 (tm-30) REVERT: A 548 ARG cc_start: 0.7911 (mtm180) cc_final: 0.6827 (mtt180) REVERT: A 604 MET cc_start: 0.7846 (ptm) cc_final: 0.7336 (ttm) REVERT: A 653 ARG cc_start: 0.5876 (ptp-170) cc_final: 0.5545 (ttp-170) REVERT: A 1074 LYS cc_start: 0.7478 (mtpp) cc_final: 0.7000 (mtmm) outliers start: 10 outliers final: 7 residues processed: 98 average time/residue: 0.2647 time to fit residues: 34.6518 Evaluate side-chains 91 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1087 LYS Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1216 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 5 optimal weight: 0.0070 chunk 50 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 115 optimal weight: 0.2980 chunk 48 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 ASN ** A1155 GLN ** 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 = 0.3883 r_free = 0.3883 target = 0.168852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124865 restraints weight = 11301.396| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.49 r_work: 0.2998 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9497 Z= 0.146 Angle : 0.521 6.691 12850 Z= 0.280 Chirality : 0.040 0.139 1479 Planarity : 0.003 0.068 1640 Dihedral : 5.067 32.094 1323 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 1.22 % Allowed : 11.60 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.23), residues: 1213 helix: -1.76 (0.19), residues: 678 sheet: -1.98 (0.68), residues: 67 loop : -2.29 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 933 HIS 0.002 0.000 HIS A 784 PHE 0.022 0.001 PHE A 305 TYR 0.007 0.001 TYR A1241 ARG 0.005 0.000 ARG A1029 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8923 (tt) cc_final: 0.8619 (tp) REVERT: A 74 MET cc_start: 0.8550 (mmp) cc_final: 0.8328 (mmt) REVERT: A 368 LYS cc_start: 0.7867 (mmmm) cc_final: 0.7613 (mmmm) REVERT: A 488 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8841 (mt) REVERT: A 544 GLU cc_start: 0.7617 (pp20) cc_final: 0.7238 (tm-30) REVERT: A 548 ARG cc_start: 0.7951 (mtm180) cc_final: 0.6959 (mtt180) REVERT: A 550 MET cc_start: 0.8252 (mtp) cc_final: 0.8052 (mtp) REVERT: A 604 MET cc_start: 0.7861 (ptm) cc_final: 0.7322 (ttm) REVERT: A 653 ARG cc_start: 0.5804 (ptp-170) cc_final: 0.5464 (ttp-170) REVERT: A 783 GLU cc_start: 0.7725 (pm20) cc_final: 0.7443 (pm20) REVERT: A 1043 LEU cc_start: 0.8580 (mp) cc_final: 0.8357 (mp) REVERT: A 1074 LYS cc_start: 0.7457 (mtpp) cc_final: 0.6995 (mtmm) outliers start: 12 outliers final: 8 residues processed: 99 average time/residue: 0.2585 time to fit residues: 34.8343 Evaluate side-chains 92 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1087 LYS Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1216 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A1080 ASN ** A1155 GLN ** 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 = 0.3825 r_free = 0.3825 target = 0.163174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.118782 restraints weight = 11431.105| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.53 r_work: 0.2956 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9497 Z= 0.326 Angle : 0.621 7.077 12850 Z= 0.329 Chirality : 0.044 0.140 1479 Planarity : 0.004 0.069 1640 Dihedral : 5.562 34.981 1323 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 1.12 % Allowed : 11.60 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.22), residues: 1213 helix: -1.99 (0.18), residues: 676 sheet: -2.27 (0.65), residues: 72 loop : -2.29 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 830 HIS 0.005 0.001 HIS A 784 PHE 0.032 0.002 PHE A 69 TYR 0.013 0.002 TYR A 250 ARG 0.005 0.000 ARG A1029 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8921 (tt) cc_final: 0.8699 (tp) REVERT: A 368 LYS cc_start: 0.7875 (mmmm) cc_final: 0.7603 (mmmm) REVERT: A 438 PHE cc_start: 0.8526 (t80) cc_final: 0.8292 (t80) REVERT: A 488 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8777 (mt) REVERT: A 544 GLU cc_start: 0.7646 (pp20) cc_final: 0.7392 (tm-30) REVERT: A 548 ARG cc_start: 0.7906 (mtm180) cc_final: 0.7228 (mtt180) REVERT: A 604 MET cc_start: 0.7841 (ptm) cc_final: 0.7344 (ttm) REVERT: A 653 ARG cc_start: 0.5897 (ptp-170) cc_final: 0.5565 (ttp-170) REVERT: A 1074 LYS cc_start: 0.7391 (mtpp) cc_final: 0.6931 (mtmm) outliers start: 11 outliers final: 8 residues processed: 92 average time/residue: 0.2837 time to fit residues: 35.4599 Evaluate side-chains 89 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1087 LYS Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1216 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 44 optimal weight: 0.0060 chunk 31 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 117 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 ASN ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** 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 = 0.3891 r_free = 0.3891 target = 0.169577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124762 restraints weight = 11067.028| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.30 r_work: 0.2990 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9497 Z= 0.148 Angle : 0.542 15.907 12850 Z= 0.285 Chirality : 0.041 0.139 1479 Planarity : 0.003 0.070 1640 Dihedral : 5.133 32.491 1323 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.22 % Allowed : 11.19 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.23), residues: 1213 helix: -1.68 (0.19), residues: 677 sheet: -2.21 (0.65), residues: 72 loop : -2.17 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 185 HIS 0.002 0.000 HIS A 784 PHE 0.022 0.001 PHE A 305 TYR 0.007 0.001 TYR A 740 ARG 0.005 0.000 ARG A1029 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 368 LYS cc_start: 0.7808 (mmmm) cc_final: 0.7537 (mmmm) REVERT: A 438 PHE cc_start: 0.8386 (t80) cc_final: 0.8075 (t80) REVERT: A 488 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8631 (mt) REVERT: A 544 GLU cc_start: 0.7619 (pp20) cc_final: 0.7259 (tm-30) REVERT: A 548 ARG cc_start: 0.7969 (mtm180) cc_final: 0.6994 (mtt180) REVERT: A 550 MET cc_start: 0.8248 (mtp) cc_final: 0.8037 (mtp) REVERT: A 604 MET cc_start: 0.7786 (ptm) cc_final: 0.7236 (ttm) REVERT: A 783 GLU cc_start: 0.7712 (pm20) cc_final: 0.7422 (pm20) REVERT: A 1074 LYS cc_start: 0.7373 (mtpp) cc_final: 0.6936 (mtmm) outliers start: 12 outliers final: 9 residues processed: 95 average time/residue: 0.2615 time to fit residues: 33.9014 Evaluate side-chains 89 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1087 LYS Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1216 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 70 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 ASN ** A1093 GLN ** 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 = 0.3784 r_free = 0.3784 target = 0.160298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.116384 restraints weight = 11456.410| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.72 r_work: 0.2897 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9497 Z= 0.397 Angle : 0.680 15.227 12850 Z= 0.353 Chirality : 0.046 0.146 1479 Planarity : 0.004 0.068 1640 Dihedral : 5.685 35.258 1323 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 1.12 % Allowed : 11.70 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.22), residues: 1213 helix: -1.98 (0.19), residues: 671 sheet: -2.35 (0.65), residues: 72 loop : -2.27 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 830 HIS 0.004 0.001 HIS A 784 PHE 0.038 0.002 PHE A 69 TYR 0.016 0.002 TYR A 250 ARG 0.006 0.001 ARG A1029 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.942 Fit side-chains REVERT: A 368 LYS cc_start: 0.7887 (mmmm) cc_final: 0.7606 (mmmm) REVERT: A 438 PHE cc_start: 0.8348 (t80) cc_final: 0.8001 (t80) REVERT: A 488 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8827 (mt) REVERT: A 544 GLU cc_start: 0.7600 (pp20) cc_final: 0.7352 (tm-30) REVERT: A 548 ARG cc_start: 0.7947 (mtm180) cc_final: 0.7248 (mtt180) REVERT: A 604 MET cc_start: 0.7722 (ptm) cc_final: 0.7112 (ttm) REVERT: A 783 GLU cc_start: 0.7620 (pm20) cc_final: 0.7407 (pm20) REVERT: A 1074 LYS cc_start: 0.7384 (mtpp) cc_final: 0.6932 (mtmm) outliers start: 11 outliers final: 9 residues processed: 87 average time/residue: 0.2761 time to fit residues: 32.6561 Evaluate side-chains 88 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1087 LYS Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1216 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 39 optimal weight: 0.0970 chunk 17 optimal weight: 0.0970 chunk 74 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 103 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 ASN ** A1093 GLN ** 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 = 0.3868 r_free = 0.3868 target = 0.167516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.122981 restraints weight = 11264.198| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.30 r_work: 0.3061 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9497 Z= 0.132 Angle : 0.539 16.130 12850 Z= 0.283 Chirality : 0.040 0.139 1479 Planarity : 0.003 0.070 1640 Dihedral : 5.114 32.137 1323 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.02 % Allowed : 11.90 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.23), residues: 1213 helix: -1.62 (0.19), residues: 673 sheet: -2.35 (0.64), residues: 72 loop : -2.10 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 185 HIS 0.002 0.000 HIS A 784 PHE 0.023 0.001 PHE A 305 TYR 0.007 0.001 TYR A 220 ARG 0.006 0.000 ARG A1029 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4882.16 seconds wall clock time: 87 minutes 7.61 seconds (5227.61 seconds total)