Starting phenix.real_space_refine on Sat Jul 20 00:41:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woi_37690/07_2024/8woi_37690.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woi_37690/07_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_37690/07_2024/8woi_37690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woi_37690/07_2024/8woi_37690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woi_37690/07_2024/8woi_37690.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woi_37690/07_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-5388/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: 5.13, per 1000 atoms: 0.55 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: 3.07 Conformation dependent library (CDL) restraints added in 1.5 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: 1.30 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: 2.86 Time building geometry restraints manager: 3.42 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 2.440 ... (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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.330 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:2.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.280 ------------------------------------------------------------------------------- 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 : 0.901 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: 0.2777 time to fit residues: 57.7243 Evaluate side-chains 91 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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: 0.7980 chunk 91 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 GLN A 748 GLN A 758 ASN A 784 HIS A 850 GLN A 921 GLN A1041 GLN A1205 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 0.043 9497 Z= 0.194 Angle : 0.627 11.646 12850 Z= 0.337 Chirality : 0.042 0.149 1479 Planarity : 0.005 0.085 1640 Dihedral : 6.456 32.943 1323 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.63 % Allowed : 6.82 % Favored : 91.56 % 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: -5.16 (0.19), residues: 1213 helix: -3.70 (0.13), residues: 667 sheet: -2.43 (0.64), residues: 71 loop : -2.87 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 933 HIS 0.003 0.001 HIS A 937 PHE 0.027 0.002 PHE A 134 TYR 0.014 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 125 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 1.005 Fit side-chains REVERT: A 472 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7763 (mt-10) REVERT: A 488 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8780 (mt) REVERT: A 604 MET cc_start: 0.7300 (ptm) cc_final: 0.6687 (ttp) REVERT: A 815 MET cc_start: 0.7354 (mmp) cc_final: 0.7084 (mmp) outliers start: 16 outliers final: 5 residues processed: 122 average time/residue: 0.2520 time to fit residues: 41.5539 Evaluate side-chains 90 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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: 0.7980 chunk 34 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 850 GLN A 921 GLN A1032 ASN A1188 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9497 Z= 0.278 Angle : 0.653 12.675 12850 Z= 0.346 Chirality : 0.043 0.144 1479 Planarity : 0.004 0.076 1640 Dihedral : 6.213 36.177 1323 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 1.12 % Allowed : 9.56 % Favored : 89.32 % 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: -4.40 (0.21), residues: 1213 helix: -3.05 (0.16), residues: 676 sheet: -1.80 (0.72), residues: 64 loop : -2.63 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 933 HIS 0.006 0.001 HIS A 937 PHE 0.029 0.002 PHE A 69 TYR 0.013 0.002 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 103 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 1.047 Fit side-chains REVERT: A 438 PHE cc_start: 0.7970 (t80) cc_final: 0.7763 (t80) REVERT: A 472 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7759 (mt-10) REVERT: A 488 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8778 (mt) REVERT: A 548 ARG cc_start: 0.7731 (mtm180) cc_final: 0.7408 (mtt180) REVERT: A 604 MET cc_start: 0.7197 (ptm) cc_final: 0.6526 (ttm) REVERT: A 680 ASN cc_start: 0.9082 (t0) cc_final: 0.8829 (t0) REVERT: A 708 MET cc_start: 0.8710 (tmm) cc_final: 0.8357 (ttt) REVERT: A 1074 LYS cc_start: 0.7565 (mtpp) cc_final: 0.7048 (mtmm) outliers start: 11 outliers final: 7 residues processed: 101 average time/residue: 0.2604 time to fit residues: 35.8312 Evaluate side-chains 83 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 SER 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 755 MET 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: 4.9990 chunk 82 optimal weight: 0.2980 chunk 57 optimal weight: 5.9990 chunk 12 optimal weight: 0.1980 chunk 52 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 116 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.8008 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9497 Z= 0.144 Angle : 0.549 10.378 12850 Z= 0.293 Chirality : 0.040 0.145 1479 Planarity : 0.004 0.074 1640 Dihedral : 5.586 32.590 1323 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.32 % Allowed : 10.17 % Favored : 88.50 % 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: -3.85 (0.22), residues: 1213 helix: -2.49 (0.18), residues: 680 sheet: -2.03 (0.68), residues: 67 loop : -2.50 (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 A1205 PHE 0.020 0.001 PHE A 305 TYR 0.009 0.001 TYR A 102 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 96 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 1.051 Fit side-chains REVERT: A 488 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8773 (mt) REVERT: A 518 MET cc_start: 0.7900 (tpt) cc_final: 0.7697 (tpt) REVERT: A 548 ARG cc_start: 0.7699 (mtm180) cc_final: 0.7405 (mtt180) REVERT: A 604 MET cc_start: 0.7106 (ptm) cc_final: 0.6522 (ttm) REVERT: A 680 ASN cc_start: 0.8959 (t0) cc_final: 0.8755 (t0) REVERT: A 708 MET cc_start: 0.8632 (tmm) cc_final: 0.8359 (ttt) REVERT: A 1074 LYS cc_start: 0.7656 (mtpp) cc_final: 0.7226 (mtmm) outliers start: 13 outliers final: 7 residues processed: 95 average time/residue: 0.2498 time to fit residues: 32.6061 Evaluate side-chains 85 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 241 VAL 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 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 66 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9497 Z= 0.176 Angle : 0.553 9.000 12850 Z= 0.296 Chirality : 0.041 0.140 1479 Planarity : 0.004 0.066 1640 Dihedral : 5.455 34.389 1323 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.73 % Allowed : 11.39 % Favored : 86.88 % 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: -3.62 (0.22), residues: 1213 helix: -2.23 (0.18), residues: 681 sheet: -2.08 (0.67), residues: 67 loop : -2.49 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 933 HIS 0.002 0.000 HIS A 937 PHE 0.020 0.001 PHE A 438 TYR 0.009 0.001 TYR A 740 ARG 0.005 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 101 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 488 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8776 (mt) REVERT: A 548 ARG cc_start: 0.7614 (mtm180) cc_final: 0.7377 (mtt180) REVERT: A 604 MET cc_start: 0.7194 (ptm) cc_final: 0.6603 (ttm) REVERT: A 708 MET cc_start: 0.8663 (tmm) cc_final: 0.8367 (ttt) REVERT: A 1074 LYS cc_start: 0.7576 (mtpp) cc_final: 0.7086 (mtmm) outliers start: 17 outliers final: 12 residues processed: 97 average time/residue: 0.2609 time to fit residues: 34.5585 Evaluate side-chains 92 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 191 SER 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 755 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 117 optimal weight: 0.0980 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 0.0670 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.3980 chunk 112 optimal weight: 0.7980 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 ASN ** 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: 0.7978 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9497 Z= 0.125 Angle : 0.510 7.546 12850 Z= 0.273 Chirality : 0.040 0.139 1479 Planarity : 0.003 0.069 1640 Dihedral : 5.090 31.401 1323 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.63 % Allowed : 11.50 % Favored : 86.88 % 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: -3.28 (0.23), residues: 1213 helix: -1.92 (0.19), residues: 675 sheet: -2.04 (0.68), residues: 67 loop : -2.37 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 185 HIS 0.001 0.000 HIS A1205 PHE 0.020 0.001 PHE A 305 TYR 0.007 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 102 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 488 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8690 (mt) REVERT: A 544 GLU cc_start: 0.6727 (pp20) cc_final: 0.6293 (tm-30) REVERT: A 548 ARG cc_start: 0.7567 (mtm180) cc_final: 0.6525 (mtt180) REVERT: A 604 MET cc_start: 0.7179 (ptm) cc_final: 0.6524 (ttm) REVERT: A 1074 LYS cc_start: 0.7613 (mtpp) cc_final: 0.7229 (mtmm) outliers start: 16 outliers final: 9 residues processed: 100 average time/residue: 0.2486 time to fit residues: 34.2523 Evaluate side-chains 86 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 191 SER 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 755 MET 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: 0.7980 chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 69 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 680 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9497 Z= 0.161 Angle : 0.529 7.088 12850 Z= 0.282 Chirality : 0.040 0.138 1479 Planarity : 0.003 0.063 1640 Dihedral : 5.099 33.829 1323 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 1.53 % Allowed : 11.80 % Favored : 86.67 % 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: -3.09 (0.23), residues: 1213 helix: -1.74 (0.19), residues: 673 sheet: -2.03 (0.68), residues: 67 loop : -2.31 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 684 HIS 0.002 0.000 HIS A 937 PHE 0.027 0.001 PHE A 438 TYR 0.009 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 97 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 488 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8596 (mt) REVERT: A 548 ARG cc_start: 0.7589 (mtm180) cc_final: 0.7331 (mtt180) REVERT: A 604 MET cc_start: 0.7160 (ptm) cc_final: 0.6454 (ttm) REVERT: A 1074 LYS cc_start: 0.7646 (mtpp) cc_final: 0.7236 (mtmm) outliers start: 15 outliers final: 12 residues processed: 94 average time/residue: 0.2629 time to fit residues: 33.6201 Evaluate side-chains 89 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 192 VAL 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 605 VAL Chi-restraints excluded: chain A residue 755 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 10 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 111 optimal weight: 0.0270 chunk 101 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 overall best weight: 1.1242 ------------------------------------------------------------------------------- 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** ** A 680 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: 0.8048 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9497 Z= 0.216 Angle : 0.571 15.128 12850 Z= 0.299 Chirality : 0.042 0.140 1479 Planarity : 0.004 0.069 1640 Dihedral : 5.247 33.533 1323 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.73 % Allowed : 12.21 % Favored : 86.06 % 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: -3.06 (0.23), residues: 1213 helix: -1.72 (0.19), residues: 674 sheet: -2.01 (0.68), residues: 67 loop : -2.31 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 933 HIS 0.003 0.001 HIS A 937 PHE 0.022 0.001 PHE A 69 TYR 0.010 0.001 TYR A 740 ARG 0.006 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 98 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 488 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8585 (mt) REVERT: A 544 GLU cc_start: 0.7071 (pp20) cc_final: 0.6715 (tm-30) REVERT: A 548 ARG cc_start: 0.7654 (mtm180) cc_final: 0.6600 (mtt180) REVERT: A 604 MET cc_start: 0.7130 (ptm) cc_final: 0.6431 (ttm) REVERT: A 1074 LYS cc_start: 0.7657 (mtpp) cc_final: 0.7239 (mtmm) outliers start: 17 outliers final: 15 residues processed: 95 average time/residue: 0.2506 time to fit residues: 32.5282 Evaluate side-chains 92 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 192 VAL 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 755 MET 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: 10.0000 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 0.0670 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 102 optimal weight: 0.1980 chunk 108 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8004 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9497 Z= 0.140 Angle : 0.529 14.925 12850 Z= 0.277 Chirality : 0.040 0.136 1479 Planarity : 0.003 0.065 1640 Dihedral : 5.006 33.221 1323 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.53 % Allowed : 12.51 % Favored : 85.96 % 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: -2.87 (0.23), residues: 1213 helix: -1.55 (0.20), residues: 673 sheet: -1.95 (0.70), residues: 67 loop : -2.24 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 933 HIS 0.002 0.000 HIS A1205 PHE 0.022 0.001 PHE A 305 TYR 0.008 0.001 TYR A 740 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 93 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 488 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8626 (mt) REVERT: A 548 ARG cc_start: 0.7616 (mtm180) cc_final: 0.7119 (mtt180) REVERT: A 604 MET cc_start: 0.7133 (ptm) cc_final: 0.6416 (ttm) REVERT: A 1074 LYS cc_start: 0.7612 (mtpp) cc_final: 0.7236 (mtmm) outliers start: 15 outliers final: 14 residues processed: 90 average time/residue: 0.2368 time to fit residues: 29.8817 Evaluate side-chains 90 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 191 SER 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 487 THR 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 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 54 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 GLN ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9497 Z= 0.241 Angle : 0.584 15.459 12850 Z= 0.305 Chirality : 0.042 0.141 1479 Planarity : 0.004 0.068 1640 Dihedral : 5.236 33.988 1323 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 1.63 % Allowed : 12.72 % Favored : 85.66 % 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: -2.94 (0.23), residues: 1213 helix: -1.62 (0.19), residues: 667 sheet: -1.97 (0.71), residues: 67 loop : -2.25 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 933 HIS 0.002 0.001 HIS A 937 PHE 0.024 0.001 PHE A 69 TYR 0.011 0.001 TYR A 250 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 90 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 488 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8673 (mt) REVERT: A 604 MET cc_start: 0.7130 (ptm) cc_final: 0.6366 (ttm) REVERT: A 1074 LYS cc_start: 0.7610 (mtpp) cc_final: 0.7222 (mtmm) outliers start: 16 outliers final: 14 residues processed: 87 average time/residue: 0.2485 time to fit residues: 29.5759 Evaluate side-chains 90 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 191 SER 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 487 THR 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 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 88 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 0.0970 chunk 84 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** 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 = 0.3869 r_free = 0.3869 target = 0.167828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.123235 restraints weight = 11147.182| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.18 r_work: 0.3007 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9497 Z= 0.149 Angle : 0.534 14.838 12850 Z= 0.281 Chirality : 0.040 0.136 1479 Planarity : 0.003 0.065 1640 Dihedral : 5.012 33.309 1323 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 1.42 % Allowed : 13.02 % Favored : 85.55 % 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: -2.70 (0.23), residues: 1213 helix: -1.41 (0.20), residues: 664 sheet: -2.01 (0.70), residues: 67 loop : -2.14 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 933 HIS 0.002 0.000 HIS A1014 PHE 0.027 0.001 PHE A 438 TYR 0.008 0.001 TYR A 740 ARG 0.004 0.000 ARG A1029 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2128.42 seconds wall clock time: 38 minutes 45.53 seconds (2325.53 seconds total)