Starting phenix.real_space_refine on Sun Aug 4 01:49:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woi_37690/08_2024/8woi_37690.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woi_37690/08_2024/8woi_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woi_37690/08_2024/8woi_37690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woi_37690/08_2024/8woi_37690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woi_37690/08_2024/8woi_37690.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woi_37690/08_2024/8woi_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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 5.27, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.7 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: 1.35 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: 2.78 Time building geometry restraints manager: 3.73 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: 73.63 - 86.32: 2 86.32 - 99.01: 5 99.01 - 111.70: 4119 111.70 - 124.39: 8573 124.39 - 137.08: 151 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: 1.170 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.790 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.210 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 0.932 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: 0.2878 time to fit residues: 60.2685 Evaluate side-chains 91 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 0.938 Fit side-chains REVERT: A 339 MET cc_start: 0.8191 (mmm) cc_final: 0.7990 (mmm) REVERT: A 488 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8662 (mt) REVERT: A 604 MET cc_start: 0.7300 (ptm) cc_final: 0.6690 (ttp) REVERT: A 815 MET cc_start: 0.7352 (mmp) cc_final: 0.7088 (mmp) outliers start: 15 outliers final: 5 residues processed: 121 average time/residue: 0.2485 time to fit residues: 40.6440 Evaluate side-chains 90 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 61 optimal weight: 0.0170 chunk 34 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A1032 ASN ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9497 Z= 0.199 Angle : 0.606 13.172 12850 Z= 0.323 Chirality : 0.042 0.143 1479 Planarity : 0.004 0.074 1640 Dihedral : 5.972 34.385 1323 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 1.12 % Allowed : 9.36 % Favored : 89.52 % 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: -4.39 (0.20), residues: 1213 helix: -2.99 (0.16), residues: 680 sheet: -1.95 (0.71), residues: 66 loop : -2.68 (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 0.022 0.002 PHE A 438 TYR 0.010 0.001 TYR A1062 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 102 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 1.056 Fit side-chains REVERT: A 305 PHE cc_start: 0.8151 (t80) cc_final: 0.7942 (t80) REVERT: A 488 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8650 (mt) REVERT: A 604 MET cc_start: 0.7262 (ptm) cc_final: 0.6611 (ttm) REVERT: A 1074 LYS cc_start: 0.7637 (mtpp) cc_final: 0.7130 (mtmm) outliers start: 11 outliers final: 5 residues processed: 99 average time/residue: 0.2484 time to fit residues: 34.0612 Evaluate side-chains 83 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 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 108 optimal weight: 0.0010 chunk 82 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 97 optimal weight: 0.3980 overall best weight: 0.4386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9497 Z= 0.133 Angle : 0.541 10.023 12850 Z= 0.291 Chirality : 0.040 0.149 1479 Planarity : 0.004 0.071 1640 Dihedral : 5.444 31.446 1323 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.42 % Allowed : 9.36 % Favored : 89.22 % 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: -3.78 (0.22), residues: 1213 helix: -2.39 (0.18), residues: 682 sheet: -1.88 (0.71), residues: 66 loop : -2.55 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 933 HIS 0.002 0.000 HIS A 937 PHE 0.020 0.001 PHE A 438 TYR 0.008 0.001 TYR A1241 ARG 0.004 0.000 ARG A1029 *********************** 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 99 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 1.068 Fit side-chains REVERT: A 488 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8621 (mt) REVERT: A 548 ARG cc_start: 0.7747 (mtm180) cc_final: 0.6917 (mtt180) REVERT: A 604 MET cc_start: 0.7090 (ptm) cc_final: 0.6511 (ttm) REVERT: A 653 ARG cc_start: 0.6049 (ttp-170) cc_final: 0.5755 (ttp-170) REVERT: A 708 MET cc_start: 0.8578 (tmm) cc_final: 0.8366 (ttt) outliers start: 14 outliers final: 6 residues processed: 96 average time/residue: 0.2385 time to fit residues: 31.6128 Evaluate side-chains 81 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 487 THR Chi-restraints excluded: chain A residue 488 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 104 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3134 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= 0.199 Angle : 0.563 8.284 12850 Z= 0.301 Chirality : 0.041 0.142 1479 Planarity : 0.004 0.065 1640 Dihedral : 5.425 33.549 1323 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.73 % Allowed : 10.99 % 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: -3.56 (0.22), residues: 1213 helix: -2.18 (0.18), residues: 680 sheet: -1.96 (0.68), residues: 67 loop : -2.49 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 933 HIS 0.003 0.000 HIS A 937 PHE 0.022 0.001 PHE A 438 TYR 0.009 0.001 TYR A 740 ARG 0.003 0.000 ARG A 548 *********************** 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 fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.922 Fit side-chains REVERT: A 368 LYS cc_start: 0.8097 (mmmm) cc_final: 0.7888 (mmmm) REVERT: A 488 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8768 (mt) REVERT: A 604 MET cc_start: 0.7163 (ptm) cc_final: 0.6549 (ttm) REVERT: A 653 ARG cc_start: 0.6310 (ttp-170) cc_final: 0.6020 (ttp-170) REVERT: A 708 MET cc_start: 0.8639 (tmm) cc_final: 0.8364 (ttt) REVERT: A 1074 LYS cc_start: 0.7688 (mtpp) cc_final: 0.7276 (mtmm) outliers start: 17 outliers final: 8 residues processed: 101 average time/residue: 0.2420 time to fit residues: 33.3059 Evaluate side-chains 89 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 487 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 overall best weight: 1.9944 ------------------------------------------------------------------------------- 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 ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9497 Z= 0.362 Angle : 0.664 7.861 12850 Z= 0.352 Chirality : 0.045 0.143 1479 Planarity : 0.004 0.071 1640 Dihedral : 5.860 34.983 1323 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 1.32 % Allowed : 11.39 % 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: -3.70 (0.22), residues: 1213 helix: -2.33 (0.18), residues: 669 sheet: -2.29 (0.63), residues: 70 loop : -2.44 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 933 HIS 0.005 0.001 HIS A 937 PHE 0.040 0.002 PHE A 69 TYR 0.016 0.002 TYR A 250 ARG 0.005 0.001 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 98 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.961 Fit side-chains REVERT: A 368 LYS cc_start: 0.8090 (mmmm) cc_final: 0.7870 (mmmm) REVERT: A 488 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8666 (mt) REVERT: A 604 MET cc_start: 0.7218 (ptm) cc_final: 0.6568 (ttm) REVERT: A 708 MET cc_start: 0.8743 (tmm) cc_final: 0.8319 (ttt) REVERT: A 1074 LYS cc_start: 0.7661 (mtpp) cc_final: 0.7228 (mtmm) outliers start: 13 outliers final: 10 residues processed: 96 average time/residue: 0.2585 time to fit residues: 33.8860 Evaluate side-chains 92 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 487 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 1057 MET 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 13 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 116 optimal weight: 0.0000 chunk 72 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 53 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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** A 575 GLN 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3409 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= 0.158 Angle : 0.546 6.882 12850 Z= 0.294 Chirality : 0.041 0.142 1479 Planarity : 0.003 0.067 1640 Dihedral : 5.377 32.936 1323 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.42 % Allowed : 11.90 % Favored : 86.67 % 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: -3.34 (0.22), residues: 1213 helix: -1.99 (0.19), residues: 675 sheet: -2.39 (0.62), residues: 72 loop : -2.29 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 933 HIS 0.002 0.000 HIS A 51 PHE 0.021 0.001 PHE A 305 TYR 0.008 0.001 TYR A 740 ARG 0.006 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 99 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 1.073 Fit side-chains REVERT: A 368 LYS cc_start: 0.8051 (mmmm) cc_final: 0.7828 (mmmm) REVERT: A 488 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8594 (mt) REVERT: A 604 MET cc_start: 0.7202 (ptm) cc_final: 0.6506 (ttm) REVERT: A 708 MET cc_start: 0.8623 (tmm) cc_final: 0.8323 (ttt) REVERT: A 1074 LYS cc_start: 0.7631 (mtpp) cc_final: 0.7156 (mtmm) outliers start: 14 outliers final: 9 residues processed: 96 average time/residue: 0.2427 time to fit residues: 32.6835 Evaluate side-chains 91 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 487 THR 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 35 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 111 optimal weight: 0.0070 chunk 101 optimal weight: 10.0000 chunk 108 optimal weight: 0.4980 overall best weight: 0.8600 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9497 Z= 0.184 Angle : 0.562 16.181 12850 Z= 0.295 Chirality : 0.041 0.139 1479 Planarity : 0.003 0.066 1640 Dihedral : 5.249 33.004 1323 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.02 % Allowed : 12.21 % Favored : 86.78 % 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: -3.14 (0.23), residues: 1213 helix: -1.82 (0.19), residues: 677 sheet: -2.26 (0.63), residues: 72 loop : -2.24 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 933 HIS 0.002 0.000 HIS A 784 PHE 0.021 0.001 PHE A 305 TYR 0.009 0.001 TYR A 740 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 96 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.962 Fit side-chains REVERT: A 368 LYS cc_start: 0.8144 (mmmm) cc_final: 0.7925 (mmmm) REVERT: A 488 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8533 (mt) REVERT: A 604 MET cc_start: 0.7144 (ptm) cc_final: 0.6445 (ttm) REVERT: A 708 MET cc_start: 0.8621 (tmm) cc_final: 0.8370 (ttt) REVERT: A 1074 LYS cc_start: 0.7607 (mtpp) cc_final: 0.7127 (mtmm) outliers start: 10 outliers final: 9 residues processed: 94 average time/residue: 0.2801 time to fit residues: 36.1602 Evaluate side-chains 90 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.2980 chunk 65 optimal weight: 0.0270 chunk 47 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 108 optimal weight: 0.0670 chunk 71 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.4776 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9497 Z= 0.133 Angle : 0.530 14.812 12850 Z= 0.278 Chirality : 0.040 0.139 1479 Planarity : 0.003 0.066 1640 Dihedral : 4.989 31.498 1323 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.02 % Allowed : 12.51 % Favored : 86.47 % 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: -2.84 (0.23), residues: 1213 helix: -1.57 (0.20), residues: 673 sheet: -2.23 (0.63), residues: 72 loop : -2.10 (0.28), 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 51 PHE 0.022 0.001 PHE A 305 TYR 0.008 0.001 TYR A 463 ARG 0.006 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 97 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.996 Fit side-chains REVERT: A 368 LYS cc_start: 0.8223 (mmmm) cc_final: 0.7999 (mmmm) REVERT: A 488 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8548 (mt) REVERT: A 604 MET cc_start: 0.7147 (ptm) cc_final: 0.6403 (ttm) REVERT: A 1074 LYS cc_start: 0.7660 (mtpp) cc_final: 0.7186 (mtmm) REVERT: A 1093 GLN cc_start: 0.7060 (tp40) cc_final: 0.6848 (mm110) outliers start: 10 outliers final: 9 residues processed: 95 average time/residue: 0.2421 time to fit residues: 31.8243 Evaluate side-chains 90 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 192 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 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 54 optimal weight: 0.0470 chunk 79 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 110 optimal weight: 0.4980 chunk 95 optimal weight: 0.8980 chunk 9 optimal weight: 0.1980 chunk 74 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.5280 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3730 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= 0.138 Angle : 0.531 15.527 12850 Z= 0.277 Chirality : 0.040 0.139 1479 Planarity : 0.003 0.065 1640 Dihedral : 4.884 31.613 1323 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.22 % Allowed : 12.61 % Favored : 86.16 % 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: -2.66 (0.24), residues: 1213 helix: -1.42 (0.20), residues: 667 sheet: -2.19 (0.64), residues: 72 loop : -2.01 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 684 HIS 0.002 0.000 HIS A 51 PHE 0.023 0.001 PHE A 305 TYR 0.008 0.001 TYR A 740 ARG 0.006 0.000 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 94 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.912 Fit side-chains REVERT: A 368 LYS cc_start: 0.8252 (mmmm) cc_final: 0.8022 (mmmm) REVERT: A 488 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8559 (mt) REVERT: A 604 MET cc_start: 0.7117 (ptm) cc_final: 0.6418 (ttm) REVERT: A 1074 LYS cc_start: 0.7655 (mtpp) cc_final: 0.7139 (mtmm) outliers start: 12 outliers final: 9 residues processed: 92 average time/residue: 0.2535 time to fit residues: 31.6373 Evaluate side-chains 89 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 192 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 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 88 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.169781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.125526 restraints weight = 11002.205| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.35 r_work: 0.3001 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9497 Z= 0.173 Angle : 0.544 14.498 12850 Z= 0.284 Chirality : 0.041 0.139 1479 Planarity : 0.003 0.066 1640 Dihedral : 4.958 32.564 1323 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.42 % Allowed : 12.21 % Favored : 86.37 % 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: -2.63 (0.24), residues: 1213 helix: -1.39 (0.20), residues: 667 sheet: -2.17 (0.64), residues: 72 loop : -2.01 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 283 HIS 0.002 0.000 HIS A 51 PHE 0.022 0.001 PHE A 305 TYR 0.009 0.001 TYR A 740 ARG 0.006 0.000 ARG A1029 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2095.09 seconds wall clock time: 37 minutes 47.94 seconds (2267.94 seconds total)