Starting phenix.real_space_refine on Fri Oct 23 22:49:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6psy_20468/10_2026/6psy_20468.cif Found real_map, /net/cci-nas-00/data/ceres_data/6psy_20468/10_2026/6psy_20468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6psy_20468/10_2026/6psy_20468.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6psy_20468/10_2026/6psy_20468.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6psy_20468/10_2026/6psy_20468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6psy_20468/10_2026/6psy_20468.map" model { file = "/net/cci-nas-00/data/ceres_data/6psy_20468/10_2026/6psy_20468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6psy_20468/10_2026/6psy_20468.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 49 5.16 5 C 7454 2.51 5 N 1891 2.21 5 O 2146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11540 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1090, 8725 Classifications: {'peptide': 1090} Link IDs: {'PTRANS': 29, 'TRANS': 1060} Chain breaks: 2 Chain: "E" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2759 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 21, 'TRANS': 317} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.55, per 1000 atoms: 0.22 Number of scatterers: 11540 At special positions: 0 Unit cell: (155.379, 94.668, 128.625, 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 49 16.00 O 2146 8.00 N 1891 7.00 C 7454 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 80 " - pdb=" SG CYS E 123 " distance=2.03 Simple disulfide: pdb=" SG CYS E 176 " - pdb=" SG CYS E 190 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN E 199 " " NAG E 403 " - " ASN E 216 " " NAG E 404 " - " ASN E 288 " Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 559.1 milliseconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2698 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 11 sheets defined 45.8% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 212 through 223 removed outlier: 3.750A pdb=" N LYS A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 236 removed outlier: 3.765A pdb=" N LEU A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 248 through 281 removed outlier: 4.173A pdb=" N SER A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 331 removed outlier: 3.899A pdb=" N LEU A 331 " --> pdb=" O PRO A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.622A pdb=" N GLN A 399 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET A 400 " --> pdb=" O PRO A 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 400' Processing helix chain 'A' and resid 438 through 473 removed outlier: 3.672A pdb=" N ILE A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 502 Processing helix chain 'A' and resid 503 through 506 removed outlier: 3.908A pdb=" N VAL A 506 " --> pdb=" O SER A 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 506' Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 600 through 612 removed outlier: 3.579A pdb=" N LEU A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 633 removed outlier: 3.526A pdb=" N ALA A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 664 Processing helix chain 'A' and resid 723 through 728 Processing helix chain 'A' and resid 729 through 731 No H-bonds generated for 'chain 'A' and resid 729 through 731' Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'A' and resid 738 through 751 Processing helix chain 'A' and resid 765 through 781 removed outlier: 3.617A pdb=" N THR A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 797 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 838 through 849 Processing helix chain 'A' and resid 867 through 881 removed outlier: 4.140A pdb=" N ARG A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 892 removed outlier: 3.651A pdb=" N THR A 892 " --> pdb=" O ASP A 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 889 through 892' Processing helix chain 'A' and resid 899 through 904 removed outlier: 3.682A pdb=" N PHE A 904 " --> pdb=" O LYS A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 919 removed outlier: 4.326A pdb=" N VAL A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 944 removed outlier: 3.926A pdb=" N ALA A 935 " --> pdb=" O PRO A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.539A pdb=" N ARG A 981 " --> pdb=" O MET A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 999 removed outlier: 4.339A pdb=" N LYS A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1023 removed outlier: 3.810A pdb=" N ILE A1008 " --> pdb=" O SER A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1029 Processing helix chain 'A' and resid 1029 through 1034 removed outlier: 4.201A pdb=" N ALA A1034 " --> pdb=" O VAL A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1050 removed outlier: 3.617A pdb=" N MET A1046 " --> pdb=" O GLU A1042 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A1047 " --> pdb=" O SER A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1063 removed outlier: 3.807A pdb=" N PHE A1059 " --> pdb=" O VAL A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1076 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 1080 through 1085 removed outlier: 3.581A pdb=" N GLN A1084 " --> pdb=" O TYR A1080 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1080 through 1085' Processing helix chain 'A' and resid 1090 through 1116 removed outlier: 3.520A pdb=" N PHE A1094 " --> pdb=" O SER A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1120 Processing helix chain 'A' and resid 1130 through 1153 Processing helix chain 'A' and resid 1160 through 1165 Processing helix chain 'A' and resid 1165 through 1183 removed outlier: 4.122A pdb=" N LEU A1169 " --> pdb=" O ILE A1165 " (cutoff:3.500A) Proline residue: A1177 - end of helix Processing helix chain 'A' and resid 1189 through 1193 removed outlier: 3.994A pdb=" N TYR A1193 " --> pdb=" O ARG A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1200 Processing helix chain 'A' and resid 1202 through 1230 removed outlier: 4.046A pdb=" N TRP A1206 " --> pdb=" O SER A1202 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N THR A1208 " --> pdb=" O VAL A1204 " (cutoff:3.500A) Proline residue: A1213 - end of helix removed outlier: 4.350A pdb=" N ALA A1216 " --> pdb=" O LEU A1212 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A1228 " --> pdb=" O LYS A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1240 Processing helix chain 'A' and resid 1254 through 1262 removed outlier: 3.533A pdb=" N LYS A1262 " --> pdb=" O ASN A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1284 removed outlier: 3.537A pdb=" N GLY A1283 " --> pdb=" O ALA A1280 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY A1284 " --> pdb=" O GLU A1281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1280 through 1284' Processing helix chain 'E' and resid 44 through 66 Proline residue: E 58 - end of helix Processing helix chain 'E' and resid 78 through 81 removed outlier: 4.585A pdb=" N ASP E 81 " --> pdb=" O SER E 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 78 through 81' Processing helix chain 'E' and resid 150 through 155 removed outlier: 4.124A pdb=" N GLN E 155 " --> pdb=" O ARG E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 163 Processing helix chain 'E' and resid 173 through 179 Proline residue: E 178 - end of helix Processing helix chain 'E' and resid 190 through 195 removed outlier: 4.167A pdb=" N ALA E 194 " --> pdb=" O CYS E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 231 Processing helix chain 'E' and resid 262 through 267 removed outlier: 4.344A pdb=" N GLU E 267 " --> pdb=" O ILE E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 273 removed outlier: 3.692A pdb=" N TRP E 272 " --> pdb=" O GLU E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 357 removed outlier: 3.600A pdb=" N LEU E 337 " --> pdb=" O GLY E 333 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL E 339 " --> pdb=" O LEU E 335 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA E 344 " --> pdb=" O ALA E 340 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY E 347 " --> pdb=" O CYS E 343 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE E 348 " --> pdb=" O ALA E 344 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU E 351 " --> pdb=" O GLY E 347 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU E 354 " --> pdb=" O PHE E 350 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 298 removed outlier: 3.859A pdb=" N GLU A 285 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE A 307 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 310 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE A 414 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASP A 319 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 314 through 315 removed outlier: 3.969A pdb=" N GLU A 314 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 407 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A 406 " --> pdb=" O GLU A 335 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 408 " --> pdb=" O TYR A 333 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR A 333 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 369 through 371 removed outlier: 4.118A pdb=" N GLY A 384 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 859 through 861 removed outlier: 6.644A pdb=" N LEU A 895 " --> pdb=" O ILE A 925 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL A 924 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE A 557 " --> pdb=" O TRP A 832 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU A 834 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N SER A 559 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU A 949 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL A 969 " --> pdb=" O LEU A 949 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ALA A 951 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE A 971 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLY A 953 " --> pdb=" O ILE A 971 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY A 968 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL A 987 " --> pdb=" O GLY A 968 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLY A 970 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 571 through 577 removed outlier: 5.736A pdb=" N PHE A 572 " --> pdb=" O GLU A 810 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU A 810 " --> pdb=" O PHE A 572 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU A 759 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA A 806 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU A 757 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A 808 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ARG A 755 " --> pdb=" O ALA A 808 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 637 through 640 Processing sheet with id=AA7, first strand: chain 'A' and resid 668 through 672 removed outlier: 6.964A pdb=" N VAL A 679 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ARG A 672 " --> pdb=" O VAL A 677 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL A 677 " --> pdb=" O ARG A 672 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 97 through 99 removed outlier: 3.532A pdb=" N ILE E 137 " --> pdb=" O ASN E 288 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR E 141 " --> pdb=" O LEU E 284 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU E 284 " --> pdb=" O TYR E 141 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE E 143 " --> pdb=" O TYR E 282 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N TYR E 282 " --> pdb=" O ILE E 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 90 through 91 removed outlier: 3.628A pdb=" N GLU E 90 " --> pdb=" O TRP E 111 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR E 201 " --> pdb=" O GLU E 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 90 through 91 removed outlier: 3.628A pdb=" N GLU E 90 " --> pdb=" O TRP E 111 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS E 297 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASN E 301 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL E 205 " --> pdb=" O ASN E 301 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 181 through 182 removed outlier: 6.251A pdb=" N ILE E 186 " --> pdb=" O VAL E 242 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1356 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: 2.43 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3379 1.34 - 1.46: 2998 1.46 - 1.59: 5345 1.59 - 1.71: 0 1.71 - 1.84: 79 Bond restraints: 11801 Sorted by residual: bond pdb=" C1 NAG E 403 " pdb=" O5 NAG E 403 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.20e+00 bond pdb=" C SER E 177 " pdb=" N PRO E 178 " ideal model delta sigma weight residual 1.337 1.364 -0.027 1.24e-02 6.50e+03 4.72e+00 bond pdb=" N THR A 540 " pdb=" CA THR A 540 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.54e-02 4.22e+03 4.63e+00 bond pdb=" CG1 ILE A1113 " pdb=" CD1 ILE A1113 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.32e+00 bond pdb=" C1 NAG E 404 " pdb=" O5 NAG E 404 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.30e+00 ... (remaining 11796 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 15625 3.07 - 6.13: 303 6.13 - 9.20: 51 9.20 - 12.27: 6 12.27 - 15.33: 2 Bond angle restraints: 15987 Sorted by residual: angle pdb=" N ILE E 348 " pdb=" CA ILE E 348 " pdb=" C ILE E 348 " ideal model delta sigma weight residual 112.96 107.51 5.45 1.00e+00 1.00e+00 2.97e+01 angle pdb=" C LYS A 799 " pdb=" N ASN A 800 " pdb=" CA ASN A 800 " ideal model delta sigma weight residual 122.82 129.41 -6.59 1.42e+00 4.96e-01 2.16e+01 angle pdb=" C ALA A 735 " pdb=" N ASN A 736 " pdb=" CA ASN A 736 " ideal model delta sigma weight residual 122.82 129.37 -6.55 1.42e+00 4.96e-01 2.12e+01 angle pdb=" C SER E 85 " pdb=" N THR E 86 " pdb=" CA THR E 86 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.07e+01 angle pdb=" CA LEU A 331 " pdb=" CB LEU A 331 " pdb=" CG LEU A 331 " ideal model delta sigma weight residual 116.30 131.63 -15.33 3.50e+00 8.16e-02 1.92e+01 ... (remaining 15982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.37: 6499 15.37 - 30.74: 384 30.74 - 46.11: 106 46.11 - 61.48: 6 61.48 - 76.85: 10 Dihedral angle restraints: 7005 sinusoidal: 2820 harmonic: 4185 Sorted by residual: dihedral pdb=" CA ASN A1033 " pdb=" C ASN A1033 " pdb=" N ALA A1034 " pdb=" CA ALA A1034 " ideal model delta harmonic sigma weight residual 180.00 146.18 33.82 0 5.00e+00 4.00e-02 4.57e+01 dihedral pdb=" CA LYS E 83 " pdb=" C LYS E 83 " pdb=" N ALA E 84 " pdb=" CA ALA E 84 " ideal model delta harmonic sigma weight residual -180.00 -149.49 -30.51 0 5.00e+00 4.00e-02 3.72e+01 dihedral pdb=" CA ASN E 195 " pdb=" C ASN E 195 " pdb=" N SER E 196 " pdb=" CA SER E 196 " ideal model delta harmonic sigma weight residual 180.00 151.65 28.35 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 7002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1531 0.082 - 0.165: 247 0.165 - 0.247: 27 0.247 - 0.330: 4 0.330 - 0.412: 2 Chirality restraints: 1811 Sorted by residual: chirality pdb=" CB ILE A 577 " pdb=" CA ILE A 577 " pdb=" CG1 ILE A 577 " pdb=" CG2 ILE A 577 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CB ILE A 861 " pdb=" CA ILE A 861 " pdb=" CG1 ILE A 861 " pdb=" CG2 ILE A 861 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CG LEU A 279 " pdb=" CB LEU A 279 " pdb=" CD1 LEU A 279 " pdb=" CD2 LEU A 279 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 1808 not shown) Planarity restraints: 2013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 336 " -0.028 2.00e-02 2.50e+03 2.48e-02 1.23e+01 pdb=" CG TYR E 336 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR E 336 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR E 336 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR E 336 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR E 336 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR E 336 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 336 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A1212 " -0.055 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO A1213 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A1213 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A1213 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1019 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.81e+00 pdb=" CG ASN A1019 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN A1019 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A1019 " 0.016 2.00e-02 2.50e+03 ... (remaining 2010 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2662 2.78 - 3.31: 10718 3.31 - 3.84: 19959 3.84 - 4.37: 24460 4.37 - 4.90: 40687 Nonbonded interactions: 98486 Sorted by model distance: nonbonded pdb=" O VAL A1136 " pdb=" OG1 THR A1140 " model vdw 2.256 3.040 nonbonded pdb=" OG SER A 930 " pdb=" OE1 GLN A 933 " model vdw 2.258 3.040 nonbonded pdb=" O PHE A 230 " pdb=" OG SER A 234 " model vdw 2.276 3.040 nonbonded pdb=" OG SER E 122 " pdb=" OD1 ASN E 301 " model vdw 2.288 3.040 nonbonded pdb=" OD1 ASN A 624 " pdb=" OH TYR A 667 " model vdw 2.298 3.040 ... (remaining 98481 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.530 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 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 : 0.007 0.092 11807 Z= 0.284 Angle : 1.081 15.332 16003 Z= 0.566 Chirality : 0.062 0.412 1811 Planarity : 0.007 0.082 2010 Dihedral : 11.336 76.847 4301 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 0.40 % Allowed : 4.28 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.87 (0.17), residues: 1421 helix: -3.70 (0.12), residues: 585 sheet: -2.48 (0.35), residues: 190 loop : -2.89 (0.21), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 151 TYR 0.055 0.004 TYR E 336 PHE 0.038 0.004 PHE E 311 TRP 0.042 0.004 TRP E 247 HIS 0.012 0.002 HIS A1104 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.28 (11801) covalent geometry : angle 1.07853 / 0.57 (15987) SS BOND : bond 0.01261 / 0.60 ( 2) SS BOND : angle 3.16789 / 2.40 ( 4) hydrogen bonds : bond 0.17239 / 11.13 ( 462) hydrogen bonds : angle 10.59282 / 7.33 ( 1356) link_BETA1-4 : bond 0.00273 / 0.14 ( 1) link_BETA1-4 : angle 1.39259 / 1.15 ( 3) link_NAG-ASN : bond 0.00657 / 0.33 ( 3) link_NAG-ASN : angle 2.57339 / 1.98 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 327 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 ILE cc_start: 0.7535 (mt) cc_final: 0.7306 (mm) REVERT: A 329 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6232 (mm-30) REVERT: A 386 MET cc_start: 0.7608 (ttm) cc_final: 0.7312 (mtp) REVERT: A 423 GLU cc_start: 0.7260 (tt0) cc_final: 0.7016 (tt0) REVERT: A 442 LYS cc_start: 0.7478 (mttt) cc_final: 0.7268 (mtpt) REVERT: A 456 ILE cc_start: 0.8165 (tp) cc_final: 0.7859 (mm) REVERT: A 606 ASP cc_start: 0.6911 (t0) cc_final: 0.6516 (m-30) REVERT: A 629 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7273 (tt) REVERT: A 649 GLN cc_start: 0.7406 (mt0) cc_final: 0.7171 (mt0) REVERT: A 830 LYS cc_start: 0.7842 (mttt) cc_final: 0.7589 (mtpm) REVERT: A 898 ASP cc_start: 0.7782 (m-30) cc_final: 0.7535 (m-30) REVERT: A 994 LYS cc_start: 0.7886 (tmtt) cc_final: 0.7309 (ttmt) REVERT: A 1066 GLN cc_start: 0.7621 (pt0) cc_final: 0.7302 (mt0) REVERT: A 1230 TYR cc_start: 0.7283 (m-80) cc_final: 0.6887 (m-80) REVERT: A 1231 GLU cc_start: 0.5963 (tt0) cc_final: 0.5245 (tm-30) REVERT: E 86 THR cc_start: 0.8621 (t) cc_final: 0.8230 (p) REVERT: E 171 ASP cc_start: 0.7604 (m-30) cc_final: 0.7400 (m-30) REVERT: E 173 ASP cc_start: 0.7383 (t0) cc_final: 0.7170 (t0) outliers start: 5 outliers final: 3 residues processed: 330 average time/residue: 0.4840 time to fit residues: 174.6781 Evaluate side-chains 199 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 195 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1218 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 238 GLN A 274 ASN A 291 HIS A 422 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 GLN A 857 ASN A 881 ASN A 963 GLN A 966 HIS A1019 ASN A1026 GLN ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1279 GLN E 155 GLN ** E 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.184400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.148447 restraints weight = 12208.498| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.19 r_work: 0.3486 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11807 Z= 0.171 Angle : 0.690 10.266 16003 Z= 0.361 Chirality : 0.047 0.195 1811 Planarity : 0.005 0.049 2010 Dihedral : 6.250 35.766 1549 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.65 % Allowed : 12.68 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.19), residues: 1421 helix: -1.99 (0.18), residues: 587 sheet: -1.94 (0.36), residues: 187 loop : -2.51 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 437 TYR 0.021 0.002 TYR E 336 PHE 0.031 0.002 PHE A 709 TRP 0.035 0.002 TRP E 247 HIS 0.008 0.001 HIS A 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (11801) covalent geometry : angle 0.68824 / 0.36 (15987) SS BOND : bond 0.00834 / 0.41 ( 2) SS BOND : angle 1.97026 / 1.55 ( 4) hydrogen bonds : bond 0.04569 / 2.97 ( 462) hydrogen bonds : angle 5.99189 / 4.16 ( 1356) link_BETA1-4 : bond 0.00128 / 0.07 ( 1) link_BETA1-4 : angle 1.74914 / 1.52 ( 3) link_NAG-ASN : bond 0.00476 / 0.24 ( 3) link_NAG-ASN : angle 1.81191 / 1.42 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 209 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ARG cc_start: 0.7342 (mtp85) cc_final: 0.7137 (mtm110) REVERT: A 248 TYR cc_start: 0.7936 (m-80) cc_final: 0.7655 (m-80) REVERT: A 323 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6995 (mt) REVERT: A 329 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7202 (mt-10) REVERT: A 369 LYS cc_start: 0.7888 (ptmt) cc_final: 0.7509 (ptmm) REVERT: A 380 TYR cc_start: 0.8331 (m-10) cc_final: 0.8129 (m-10) REVERT: A 381 THR cc_start: 0.8192 (m) cc_final: 0.7693 (p) REVERT: A 386 MET cc_start: 0.8289 (ttm) cc_final: 0.8030 (mtp) REVERT: A 456 ILE cc_start: 0.8503 (tp) cc_final: 0.8223 (mm) REVERT: A 606 ASP cc_start: 0.6799 (t0) cc_final: 0.5897 (m-30) REVERT: A 609 LYS cc_start: 0.7154 (tptm) cc_final: 0.6860 (ttpp) REVERT: A 623 ILE cc_start: 0.7429 (pt) cc_final: 0.7205 (mt) REVERT: A 664 ASP cc_start: 0.7897 (m-30) cc_final: 0.7556 (m-30) REVERT: A 670 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6898 (pp) REVERT: A 730 ARG cc_start: 0.7600 (ptp90) cc_final: 0.7384 (ptp-110) REVERT: A 830 LYS cc_start: 0.8511 (mttt) cc_final: 0.8209 (mtpm) REVERT: A 898 ASP cc_start: 0.8272 (m-30) cc_final: 0.7826 (t70) REVERT: A 911 GLU cc_start: 0.6553 (tt0) cc_final: 0.6117 (tt0) REVERT: A 977 MET cc_start: 0.5730 (tpp) cc_final: 0.5497 (tpp) REVERT: A 994 LYS cc_start: 0.8318 (tmtt) cc_final: 0.7764 (ttmt) REVERT: A 1066 GLN cc_start: 0.7629 (pt0) cc_final: 0.7335 (mt0) REVERT: A 1159 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7569 (tttt) REVERT: A 1230 TYR cc_start: 0.7564 (m-80) cc_final: 0.7201 (m-80) REVERT: A 1231 GLU cc_start: 0.6287 (tt0) cc_final: 0.5405 (tm-30) REVERT: A 1286 GLU cc_start: 0.6774 (pt0) cc_final: 0.5980 (tp30) REVERT: E 29 ARG cc_start: 0.7842 (tpp80) cc_final: 0.7541 (mmt180) REVERT: E 86 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.7759 (p) REVERT: E 110 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8648 (mt0) REVERT: E 112 ARG cc_start: 0.8000 (ptm160) cc_final: 0.7622 (ttm170) REVERT: E 152 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7954 (ttm-80) REVERT: E 171 ASP cc_start: 0.7850 (m-30) cc_final: 0.7501 (m-30) REVERT: E 209 ILE cc_start: 0.7410 (pp) cc_final: 0.6955 (pp) REVERT: E 218 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8301 (t) REVERT: E 248 MET cc_start: 0.8310 (mmm) cc_final: 0.8034 (mmm) REVERT: E 268 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7697 (mt-10) outliers start: 46 outliers final: 19 residues processed: 232 average time/residue: 0.4789 time to fit residues: 122.4578 Evaluate side-chains 198 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1070 SER Chi-restraints excluded: chain A residue 1159 LYS Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 317 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [37, 10, 86, 78, 51, 63, 73, 112, 1, 132, 64] chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 132 optimal weight: 0.0470 chunk 64 optimal weight: 6.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 ASN A 814 GLN A1019 ASN ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 GLN E 299 GLN E 301 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.174252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.138642 restraints weight = 12234.079| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.40 r_work: 0.3337 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 11807 Z= 0.264 Angle : 0.760 11.695 16003 Z= 0.389 Chirality : 0.051 0.205 1811 Planarity : 0.005 0.048 2010 Dihedral : 6.090 33.303 1543 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 6.66 % Allowed : 13.23 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.21), residues: 1421 helix: -1.35 (0.19), residues: 593 sheet: -1.98 (0.34), residues: 209 loop : -2.14 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 943 TYR 0.030 0.003 TYR E 336 PHE 0.027 0.003 PHE E 311 TRP 0.037 0.003 TRP E 247 HIS 0.008 0.002 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.26 (11801) covalent geometry : angle 0.75665 / 0.39 (15987) SS BOND : bond 0.01015 / 0.48 ( 2) SS BOND : angle 2.31930 / 1.66 ( 4) hydrogen bonds : bond 0.04752 / 3.02 ( 462) hydrogen bonds : angle 5.49597 / 3.84 ( 1356) link_BETA1-4 : bond 0.00487 / 0.26 ( 1) link_BETA1-4 : angle 2.47570 / 2.10 ( 3) link_NAG-ASN : bond 0.00607 / 0.31 ( 3) link_NAG-ASN : angle 2.17881 / 1.85 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 187 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8319 (tm-30) cc_final: 0.8078 (tt0) REVERT: A 323 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7294 (mt) REVERT: A 329 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7609 (mt-10) REVERT: A 369 LYS cc_start: 0.7900 (ptmt) cc_final: 0.7503 (ptmm) REVERT: A 442 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7685 (mtpt) REVERT: A 456 ILE cc_start: 0.8451 (tp) cc_final: 0.8161 (mm) REVERT: A 606 ASP cc_start: 0.6917 (t0) cc_final: 0.6123 (m-30) REVERT: A 609 LYS cc_start: 0.7299 (tptm) cc_final: 0.7004 (ttpp) REVERT: A 664 ASP cc_start: 0.8079 (m-30) cc_final: 0.7725 (m-30) REVERT: A 670 ILE cc_start: 0.7519 (OUTLIER) cc_final: 0.7252 (pt) REVERT: A 730 ARG cc_start: 0.7636 (ptp90) cc_final: 0.7240 (ptm160) REVERT: A 740 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: A 748 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.7025 (m-30) REVERT: A 830 LYS cc_start: 0.8649 (mttt) cc_final: 0.8360 (mtpm) REVERT: A 898 ASP cc_start: 0.8230 (m-30) cc_final: 0.7834 (t70) REVERT: A 911 GLU cc_start: 0.7005 (tt0) cc_final: 0.6776 (tt0) REVERT: A 932 LEU cc_start: 0.7619 (tp) cc_final: 0.7381 (tt) REVERT: A 961 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8347 (tmm) REVERT: A 977 MET cc_start: 0.6051 (tpp) cc_final: 0.5532 (tpp) REVERT: A 994 LYS cc_start: 0.8248 (tmtt) cc_final: 0.7697 (ttmt) REVERT: A 1066 GLN cc_start: 0.7877 (pt0) cc_final: 0.7371 (mt0) REVERT: A 1159 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7591 (tttt) REVERT: A 1174 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8298 (mm) REVERT: A 1230 TYR cc_start: 0.7687 (m-80) cc_final: 0.7304 (m-80) REVERT: A 1231 GLU cc_start: 0.6620 (tt0) cc_final: 0.5682 (tm-30) REVERT: A 1286 GLU cc_start: 0.7078 (pt0) cc_final: 0.6145 (tp30) REVERT: E 41 SER cc_start: 0.7506 (t) cc_final: 0.7105 (p) REVERT: E 86 THR cc_start: 0.8364 (t) cc_final: 0.7866 (p) REVERT: E 110 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8642 (mt0) REVERT: E 111 TRP cc_start: 0.7265 (p-90) cc_final: 0.6918 (p90) REVERT: E 134 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7797 (mmtm) REVERT: E 154 VAL cc_start: 0.8882 (m) cc_final: 0.8547 (t) REVERT: E 168 LYS cc_start: 0.7914 (mptt) cc_final: 0.7687 (mmtm) REVERT: E 171 ASP cc_start: 0.8024 (m-30) cc_final: 0.7588 (m-30) REVERT: E 247 TRP cc_start: 0.7742 (OUTLIER) cc_final: 0.7344 (p-90) REVERT: E 248 MET cc_start: 0.8691 (mmm) cc_final: 0.8361 (mmm) REVERT: E 268 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7711 (mt-10) outliers start: 84 outliers final: 34 residues processed: 242 average time/residue: 0.4687 time to fit residues: 125.4480 Evaluate side-chains 208 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 162 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1159 LYS Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 247 TRP Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 325 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [124, 89, 61, 1, 41, 107, 52, 47, 88, 119, 112] chunk 124 optimal weight: 0.3980 chunk 89 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 52 optimal weight: 0.3980 chunk 47 optimal weight: 0.8980 chunk 88 optimal weight: 0.4980 chunk 119 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 ASN A 878 ASN A1019 ASN A1038 GLN A1131 HIS A1296 GLN ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 ASN E 299 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.179511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.143851 restraints weight = 12271.697| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.25 r_work: 0.3413 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11807 Z= 0.140 Angle : 0.618 8.302 16003 Z= 0.322 Chirality : 0.045 0.175 1811 Planarity : 0.004 0.046 2010 Dihedral : 5.600 31.547 1543 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 4.99 % Allowed : 16.16 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.21), residues: 1421 helix: -0.75 (0.20), residues: 593 sheet: -1.53 (0.37), residues: 190 loop : -2.08 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 437 TYR 0.014 0.002 TYR E 141 PHE 0.017 0.002 PHE E 317 TRP 0.029 0.002 TRP E 247 HIS 0.005 0.001 HIS A1104 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (11801) covalent geometry : angle 0.61652 / 0.32 (15987) SS BOND : bond 0.00666 / 0.32 ( 2) SS BOND : angle 1.64887 / 1.20 ( 4) hydrogen bonds : bond 0.04035 / 2.62 ( 462) hydrogen bonds : angle 5.00072 / 3.51 ( 1356) link_BETA1-4 : bond 0.00053 / 0.03 ( 1) link_BETA1-4 : angle 1.53090 / 1.27 ( 3) link_NAG-ASN : bond 0.00408 / 0.20 ( 3) link_NAG-ASN : angle 1.61547 / 1.28 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 172 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 ILE cc_start: 0.7833 (pp) cc_final: 0.7596 (pp) REVERT: A 297 LYS cc_start: 0.7778 (mttm) cc_final: 0.7369 (mtpt) REVERT: A 323 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7117 (mt) REVERT: A 324 SER cc_start: 0.8495 (t) cc_final: 0.8277 (m) REVERT: A 329 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7236 (mm-30) REVERT: A 369 LYS cc_start: 0.7958 (ptmt) cc_final: 0.7541 (ptmm) REVERT: A 373 GLU cc_start: 0.7730 (tt0) cc_final: 0.7504 (tt0) REVERT: A 381 THR cc_start: 0.8296 (m) cc_final: 0.7786 (p) REVERT: A 456 ILE cc_start: 0.8427 (tp) cc_final: 0.8146 (mt) REVERT: A 511 PHE cc_start: 0.6745 (t80) cc_final: 0.6389 (t80) REVERT: A 540 THR cc_start: 0.8377 (t) cc_final: 0.7635 (m) REVERT: A 571 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7244 (tp30) REVERT: A 606 ASP cc_start: 0.6639 (t0) cc_final: 0.5774 (m-30) REVERT: A 609 LYS cc_start: 0.7102 (tptm) cc_final: 0.6840 (ttpp) REVERT: A 664 ASP cc_start: 0.8034 (m-30) cc_final: 0.7646 (m-30) REVERT: A 717 LYS cc_start: 0.6813 (OUTLIER) cc_final: 0.6604 (ptpt) REVERT: A 830 LYS cc_start: 0.8660 (mttt) cc_final: 0.8396 (mtpm) REVERT: A 898 ASP cc_start: 0.8149 (m-30) cc_final: 0.7792 (t70) REVERT: A 932 LEU cc_start: 0.7593 (tp) cc_final: 0.7353 (tt) REVERT: A 977 MET cc_start: 0.5956 (tpp) cc_final: 0.5439 (tpp) REVERT: A 994 LYS cc_start: 0.8227 (tmtt) cc_final: 0.7701 (ttmt) REVERT: A 1066 GLN cc_start: 0.7734 (pt0) cc_final: 0.7321 (mt0) REVERT: A 1159 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7682 (tttt) REVERT: A 1174 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8214 (mm) REVERT: A 1230 TYR cc_start: 0.7524 (m-80) cc_final: 0.7212 (m-80) REVERT: A 1231 GLU cc_start: 0.6573 (tt0) cc_final: 0.5623 (tm-30) REVERT: A 1286 GLU cc_start: 0.6878 (pt0) cc_final: 0.6042 (tp30) REVERT: E 86 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.7876 (p) REVERT: E 110 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8700 (mt0) REVERT: E 111 TRP cc_start: 0.7214 (p-90) cc_final: 0.6879 (p-90) REVERT: E 147 TYR cc_start: 0.8716 (m-80) cc_final: 0.8480 (m-80) REVERT: E 154 VAL cc_start: 0.8719 (m) cc_final: 0.8379 (t) REVERT: E 171 ASP cc_start: 0.7972 (m-30) cc_final: 0.7681 (m-30) REVERT: E 193 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8012 (mp) REVERT: E 218 THR cc_start: 0.8584 (p) cc_final: 0.8381 (t) REVERT: E 247 TRP cc_start: 0.7376 (OUTLIER) cc_final: 0.6533 (p-90) REVERT: E 248 MET cc_start: 0.8546 (mmm) cc_final: 0.8226 (mmm) outliers start: 63 outliers final: 23 residues processed: 210 average time/residue: 0.4513 time to fit residues: 105.0069 Evaluate side-chains 196 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 717 LYS Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1159 LYS Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 247 TRP Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 325 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [18, 103, 130, 38, 112, 78, 45, 80, 85, 102, 65] chunk 18 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 102 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 ASN A 963 GLN A1019 ASN A1236 HIS ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.177717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.142308 restraints weight = 12230.228| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.15 r_work: 0.3403 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11807 Z= 0.157 Angle : 0.631 8.485 16003 Z= 0.325 Chirality : 0.046 0.171 1811 Planarity : 0.004 0.047 2010 Dihedral : 5.429 29.627 1543 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.91 % Allowed : 16.88 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.22), residues: 1421 helix: -0.40 (0.21), residues: 592 sheet: -1.53 (0.36), residues: 194 loop : -1.98 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 437 TYR 0.016 0.002 TYR E 147 PHE 0.017 0.002 PHE E 311 TRP 0.029 0.002 TRP E 247 HIS 0.004 0.001 HIS A1198 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (11801) covalent geometry : angle 0.62875 / 0.32 (15987) SS BOND : bond 0.00742 / 0.35 ( 2) SS BOND : angle 1.74220 / 1.22 ( 4) hydrogen bonds : bond 0.04072 / 2.64 ( 462) hydrogen bonds : angle 4.87682 / 3.43 ( 1356) link_BETA1-4 : bond 0.00101 / 0.05 ( 1) link_BETA1-4 : angle 1.94500 / 1.70 ( 3) link_NAG-ASN : bond 0.00424 / 0.21 ( 3) link_NAG-ASN : angle 1.72071 / 1.41 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 164 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 LYS cc_start: 0.6533 (tttm) cc_final: 0.6286 (tttp) REVERT: A 236 ILE cc_start: 0.7949 (pp) cc_final: 0.7714 (pp) REVERT: A 323 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7140 (mt) REVERT: A 324 SER cc_start: 0.8458 (OUTLIER) cc_final: 0.8254 (m) REVERT: A 329 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7368 (mm-30) REVERT: A 367 ASN cc_start: 0.7204 (m110) cc_final: 0.6970 (m-40) REVERT: A 369 LYS cc_start: 0.7992 (ptmt) cc_final: 0.6525 (mtpt) REVERT: A 381 THR cc_start: 0.8270 (m) cc_final: 0.7767 (p) REVERT: A 456 ILE cc_start: 0.8422 (tp) cc_final: 0.8144 (mt) REVERT: A 511 PHE cc_start: 0.6677 (t80) cc_final: 0.6326 (t80) REVERT: A 571 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7350 (tp30) REVERT: A 606 ASP cc_start: 0.6616 (t0) cc_final: 0.5733 (m-30) REVERT: A 609 LYS cc_start: 0.7072 (tptm) cc_final: 0.6800 (ttpp) REVERT: A 664 ASP cc_start: 0.8019 (m-30) cc_final: 0.7695 (m-30) REVERT: A 717 LYS cc_start: 0.6704 (OUTLIER) cc_final: 0.6449 (ptpt) REVERT: A 830 LYS cc_start: 0.8569 (mttt) cc_final: 0.8283 (mtpm) REVERT: A 898 ASP cc_start: 0.8142 (m-30) cc_final: 0.7782 (t70) REVERT: A 932 LEU cc_start: 0.7656 (tp) cc_final: 0.7403 (tt) REVERT: A 994 LYS cc_start: 0.8201 (tmtt) cc_final: 0.7676 (ttmt) REVERT: A 1046 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.6394 (mtm) REVERT: A 1066 GLN cc_start: 0.7737 (pt0) cc_final: 0.7279 (mt0) REVERT: A 1159 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7625 (tttt) REVERT: A 1174 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8194 (mm) REVERT: A 1230 TYR cc_start: 0.7569 (m-80) cc_final: 0.7257 (m-80) REVERT: A 1231 GLU cc_start: 0.6646 (tt0) cc_final: 0.5654 (tm-30) REVERT: A 1286 GLU cc_start: 0.6930 (pt0) cc_final: 0.6071 (tp30) REVERT: E 86 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.7850 (p) REVERT: E 95 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7955 (ptmt) REVERT: E 110 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8642 (mt0) REVERT: E 111 TRP cc_start: 0.7192 (p-90) cc_final: 0.6881 (p-90) REVERT: E 134 LYS cc_start: 0.8189 (mttm) cc_final: 0.7989 (mmtm) REVERT: E 154 VAL cc_start: 0.8736 (m) cc_final: 0.8459 (t) REVERT: E 171 ASP cc_start: 0.7987 (m-30) cc_final: 0.7693 (m-30) REVERT: E 193 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7933 (mt) REVERT: E 209 ILE cc_start: 0.7415 (pp) cc_final: 0.7179 (pp) REVERT: E 247 TRP cc_start: 0.7371 (OUTLIER) cc_final: 0.6587 (p-90) REVERT: E 248 MET cc_start: 0.8496 (mmm) cc_final: 0.8191 (mmm) REVERT: E 268 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7612 (mp0) outliers start: 62 outliers final: 28 residues processed: 208 average time/residue: 0.4710 time to fit residues: 107.8687 Evaluate side-chains 195 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 717 LYS Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1070 SER Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1159 LYS Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 247 TRP Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 325 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [90, 42, 125, 7, 121, 48, 128, 51, 47, 66, 134] chunk 90 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 134 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 ASN A1019 ASN ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.174974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.138677 restraints weight = 12253.917| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.37 r_work: 0.3357 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11807 Z= 0.191 Angle : 0.654 8.692 16003 Z= 0.338 Chirality : 0.047 0.211 1811 Planarity : 0.004 0.047 2010 Dihedral : 5.482 31.760 1543 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.99 % Allowed : 17.67 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.22), residues: 1421 helix: -0.29 (0.21), residues: 592 sheet: -1.35 (0.37), residues: 184 loop : -1.95 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 603 TYR 0.017 0.002 TYR A 913 PHE 0.020 0.002 PHE E 311 TRP 0.032 0.002 TRP E 247 HIS 0.006 0.001 HIS A1198 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (11801) covalent geometry : angle 0.65131 / 0.34 (15987) SS BOND : bond 0.00870 / 0.41 ( 2) SS BOND : angle 1.99081 / 1.42 ( 4) hydrogen bonds : bond 0.04212 / 2.71 ( 462) hydrogen bonds : angle 4.87140 / 3.44 ( 1356) link_BETA1-4 : bond 0.00128 / 0.07 ( 1) link_BETA1-4 : angle 2.05409 / 1.75 ( 3) link_NAG-ASN : bond 0.00444 / 0.22 ( 3) link_NAG-ASN : angle 1.94355 / 1.58 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 164 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 LYS cc_start: 0.6571 (tttm) cc_final: 0.6328 (tttp) REVERT: A 329 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7475 (mm-30) REVERT: A 367 ASN cc_start: 0.7163 (m110) cc_final: 0.6937 (m-40) REVERT: A 369 LYS cc_start: 0.7991 (ptmt) cc_final: 0.6525 (mtpt) REVERT: A 456 ILE cc_start: 0.8401 (tp) cc_final: 0.8126 (mt) REVERT: A 511 PHE cc_start: 0.6808 (t80) cc_final: 0.6427 (t80) REVERT: A 540 THR cc_start: 0.8433 (t) cc_final: 0.7718 (m) REVERT: A 571 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7282 (tp30) REVERT: A 606 ASP cc_start: 0.6614 (t0) cc_final: 0.5863 (m-30) REVERT: A 609 LYS cc_start: 0.7140 (tptm) cc_final: 0.6840 (ttpp) REVERT: A 664 ASP cc_start: 0.8058 (m-30) cc_final: 0.7723 (m-30) REVERT: A 717 LYS cc_start: 0.6835 (OUTLIER) cc_final: 0.6600 (ptpt) REVERT: A 830 LYS cc_start: 0.8572 (mttt) cc_final: 0.8246 (mtpm) REVERT: A 847 MET cc_start: 0.8412 (tpp) cc_final: 0.8197 (mmm) REVERT: A 898 ASP cc_start: 0.8139 (m-30) cc_final: 0.7791 (t70) REVERT: A 994 LYS cc_start: 0.8212 (tmtt) cc_final: 0.7654 (ttmt) REVERT: A 1046 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.6630 (mtm) REVERT: A 1066 GLN cc_start: 0.7819 (pt0) cc_final: 0.7247 (mt0) REVERT: A 1159 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7740 (tttt) REVERT: A 1174 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8236 (mm) REVERT: A 1230 TYR cc_start: 0.7782 (m-80) cc_final: 0.7455 (m-80) REVERT: A 1231 GLU cc_start: 0.6654 (tt0) cc_final: 0.5637 (tm-30) REVERT: A 1269 MET cc_start: 0.6770 (OUTLIER) cc_final: 0.5933 (tpt) REVERT: A 1286 GLU cc_start: 0.7013 (pt0) cc_final: 0.6147 (tp30) REVERT: E 73 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8581 (tp) REVERT: E 86 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.7856 (p) REVERT: E 90 GLU cc_start: 0.7756 (pt0) cc_final: 0.7525 (pt0) REVERT: E 95 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7970 (ptmt) REVERT: E 134 LYS cc_start: 0.8256 (mttm) cc_final: 0.8029 (mmtm) REVERT: E 147 TYR cc_start: 0.8866 (m-80) cc_final: 0.8609 (m-80) REVERT: E 154 VAL cc_start: 0.8772 (m) cc_final: 0.8453 (t) REVERT: E 171 ASP cc_start: 0.8009 (m-30) cc_final: 0.7709 (m-30) REVERT: E 247 TRP cc_start: 0.7472 (OUTLIER) cc_final: 0.6823 (p-90) REVERT: E 248 MET cc_start: 0.8504 (mmm) cc_final: 0.8222 (mmm) REVERT: E 268 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7591 (mp0) outliers start: 63 outliers final: 35 residues processed: 210 average time/residue: 0.4801 time to fit residues: 110.6064 Evaluate side-chains 203 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 717 LYS Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1070 SER Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1159 LYS Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1269 MET Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 247 TRP Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 325 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [40, 14, 61, 51, 71, 94, 91, 121, 49, 68, 92] chunk 40 optimal weight: 9.9990 chunk 14 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 ASN A1019 ASN E 126 GLN ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.177586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.141527 restraints weight = 12200.476| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.24 r_work: 0.3393 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11807 Z= 0.136 Angle : 0.608 7.805 16003 Z= 0.315 Chirality : 0.044 0.161 1811 Planarity : 0.004 0.046 2010 Dihedral : 5.248 31.247 1543 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.20 % Allowed : 18.78 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.22), residues: 1421 helix: -0.08 (0.21), residues: 592 sheet: -1.20 (0.38), residues: 176 loop : -1.86 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 871 TYR 0.015 0.002 TYR E 147 PHE 0.016 0.001 PHE E 317 TRP 0.028 0.001 TRP E 247 HIS 0.004 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (11801) covalent geometry : angle 0.60562 / 0.31 (15987) SS BOND : bond 0.00635 / 0.30 ( 2) SS BOND : angle 1.54868 / 1.09 ( 4) hydrogen bonds : bond 0.03899 / 2.55 ( 462) hydrogen bonds : angle 4.75591 / 3.35 ( 1356) link_BETA1-4 : bond 0.00082 / 0.04 ( 1) link_BETA1-4 : angle 1.72268 / 1.45 ( 3) link_NAG-ASN : bond 0.00383 / 0.19 ( 3) link_NAG-ASN : angle 1.68437 / 1.34 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 163 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 LYS cc_start: 0.6446 (tttm) cc_final: 0.6236 (tttp) REVERT: A 267 ILE cc_start: 0.8802 (mt) cc_final: 0.8558 (mt) REVERT: A 329 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7506 (mm-30) REVERT: A 367 ASN cc_start: 0.7126 (m110) cc_final: 0.6892 (m-40) REVERT: A 369 LYS cc_start: 0.7926 (ptmt) cc_final: 0.6594 (mtpt) REVERT: A 381 THR cc_start: 0.8263 (m) cc_final: 0.7837 (p) REVERT: A 386 MET cc_start: 0.8259 (ttp) cc_final: 0.8011 (mtp) REVERT: A 456 ILE cc_start: 0.8377 (tp) cc_final: 0.8112 (mt) REVERT: A 540 THR cc_start: 0.8386 (t) cc_final: 0.7672 (m) REVERT: A 571 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7326 (tp30) REVERT: A 606 ASP cc_start: 0.6676 (t0) cc_final: 0.5891 (m-30) REVERT: A 609 LYS cc_start: 0.7140 (tptm) cc_final: 0.6910 (pttp) REVERT: A 664 ASP cc_start: 0.8025 (m-30) cc_final: 0.7674 (m-30) REVERT: A 717 LYS cc_start: 0.6762 (OUTLIER) cc_final: 0.6488 (ptpt) REVERT: A 830 LYS cc_start: 0.8579 (mttt) cc_final: 0.8312 (mtpm) REVERT: A 847 MET cc_start: 0.8406 (tpp) cc_final: 0.8195 (mmm) REVERT: A 882 GLU cc_start: 0.6394 (tm-30) cc_final: 0.6084 (tm-30) REVERT: A 994 LYS cc_start: 0.8212 (tmtt) cc_final: 0.7668 (ttmt) REVERT: A 1046 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.6267 (mtm) REVERT: A 1066 GLN cc_start: 0.7800 (pt0) cc_final: 0.7264 (mt0) REVERT: A 1174 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8198 (mm) REVERT: A 1230 TYR cc_start: 0.7739 (m-80) cc_final: 0.7469 (m-80) REVERT: A 1231 GLU cc_start: 0.6589 (tt0) cc_final: 0.5577 (tm-30) REVERT: A 1269 MET cc_start: 0.6733 (OUTLIER) cc_final: 0.5897 (tpt) REVERT: A 1286 GLU cc_start: 0.6910 (pt0) cc_final: 0.6130 (tp30) REVERT: E 73 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8596 (tp) REVERT: E 86 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.7903 (p) REVERT: E 95 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8168 (ptmt) REVERT: E 154 VAL cc_start: 0.8701 (m) cc_final: 0.8431 (t) REVERT: E 171 ASP cc_start: 0.8050 (m-30) cc_final: 0.7715 (m-30) REVERT: E 248 MET cc_start: 0.8450 (mmm) cc_final: 0.8218 (mmm) REVERT: E 268 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: E 325 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7718 (pp) outliers start: 53 outliers final: 30 residues processed: 201 average time/residue: 0.4652 time to fit residues: 103.2482 Evaluate side-chains 193 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 717 LYS Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1269 MET Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 325 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [36, 112, 0, 130, 41, 35, 131, 99, 135, 59, 23] chunk 36 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 131 optimal weight: 0.0020 chunk 99 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 ASN A1019 ASN A1050 ASN ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.177919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.142933 restraints weight = 12221.429| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.20 r_work: 0.3416 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11807 Z= 0.135 Angle : 0.602 7.900 16003 Z= 0.312 Chirality : 0.044 0.160 1811 Planarity : 0.004 0.046 2010 Dihedral : 5.192 31.647 1543 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 4.36 % Allowed : 18.62 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.22), residues: 1421 helix: -0.05 (0.21), residues: 598 sheet: -1.18 (0.38), residues: 178 loop : -1.91 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 702 TYR 0.014 0.002 TYR A 913 PHE 0.016 0.001 PHE E 317 TRP 0.030 0.001 TRP E 247 HIS 0.003 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (11801) covalent geometry : angle 0.59959 / 0.31 (15987) SS BOND : bond 0.00633 / 0.30 ( 2) SS BOND : angle 1.51499 / 1.06 ( 4) hydrogen bonds : bond 0.03897 / 2.54 ( 462) hydrogen bonds : angle 4.73145 / 3.34 ( 1356) link_BETA1-4 : bond 0.00042 / 0.02 ( 1) link_BETA1-4 : angle 1.73130 / 1.47 ( 3) link_NAG-ASN : bond 0.00396 / 0.19 ( 3) link_NAG-ASN : angle 1.68395 / 1.34 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 161 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7541 (mm-30) REVERT: A 367 ASN cc_start: 0.7150 (m110) cc_final: 0.6916 (m-40) REVERT: A 369 LYS cc_start: 0.7897 (ptmt) cc_final: 0.6585 (mtpt) REVERT: A 381 THR cc_start: 0.8220 (m) cc_final: 0.7754 (p) REVERT: A 386 MET cc_start: 0.8267 (ttp) cc_final: 0.8044 (mtp) REVERT: A 456 ILE cc_start: 0.8365 (tp) cc_final: 0.8096 (mt) REVERT: A 540 THR cc_start: 0.8384 (t) cc_final: 0.7686 (m) REVERT: A 571 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7305 (tp30) REVERT: A 606 ASP cc_start: 0.6729 (t0) cc_final: 0.5961 (m-30) REVERT: A 609 LYS cc_start: 0.7177 (tptm) cc_final: 0.6958 (pttp) REVERT: A 664 ASP cc_start: 0.8016 (m-30) cc_final: 0.7698 (m-30) REVERT: A 717 LYS cc_start: 0.6771 (OUTLIER) cc_final: 0.6503 (ptpt) REVERT: A 830 LYS cc_start: 0.8567 (mttt) cc_final: 0.8244 (mtpm) REVERT: A 847 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8184 (mmm) REVERT: A 882 GLU cc_start: 0.6373 (tm-30) cc_final: 0.6039 (tm-30) REVERT: A 994 LYS cc_start: 0.8195 (tmtt) cc_final: 0.7634 (ttmt) REVERT: A 1046 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.6293 (mtm) REVERT: A 1066 GLN cc_start: 0.7786 (pt0) cc_final: 0.7227 (mt0) REVERT: A 1174 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8191 (mm) REVERT: A 1230 TYR cc_start: 0.7753 (m-80) cc_final: 0.7477 (m-80) REVERT: A 1231 GLU cc_start: 0.6593 (tt0) cc_final: 0.5602 (tm-30) REVERT: A 1241 MET cc_start: 0.5011 (mmm) cc_final: 0.4639 (mtt) REVERT: A 1269 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.5898 (tpt) REVERT: A 1286 GLU cc_start: 0.6806 (pt0) cc_final: 0.5998 (tp30) REVERT: E 73 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8606 (tp) REVERT: E 86 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.7927 (p) REVERT: E 95 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8184 (ptmt) REVERT: E 154 VAL cc_start: 0.8673 (m) cc_final: 0.8451 (t) REVERT: E 171 ASP cc_start: 0.8035 (m-30) cc_final: 0.7698 (m-30) REVERT: E 193 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7964 (mt) REVERT: E 247 TRP cc_start: 0.7127 (OUTLIER) cc_final: 0.6370 (p-90) REVERT: E 248 MET cc_start: 0.8409 (mmm) cc_final: 0.8148 (mmm) REVERT: E 268 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7561 (mp0) outliers start: 55 outliers final: 29 residues processed: 200 average time/residue: 0.4736 time to fit residues: 104.4496 Evaluate side-chains 197 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 717 LYS Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1269 MET Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 247 TRP Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 317 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [48, 78, 91, 13, 121, 85, 123, 32, 40, 92, 130] chunk 48 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 chunk 130 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 ASN A 699 ASN A1019 ASN ** A1050 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.177985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.141733 restraints weight = 12103.047| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.25 r_work: 0.3405 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11807 Z= 0.137 Angle : 0.602 7.938 16003 Z= 0.312 Chirality : 0.044 0.160 1811 Planarity : 0.004 0.046 2010 Dihedral : 5.144 31.213 1543 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 4.20 % Allowed : 18.94 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.22), residues: 1421 helix: 0.00 (0.21), residues: 599 sheet: -1.08 (0.39), residues: 174 loop : -1.87 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 702 TYR 0.014 0.002 TYR A 913 PHE 0.016 0.002 PHE E 317 TRP 0.030 0.001 TRP E 247 HIS 0.003 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (11801) covalent geometry : angle 0.59989 / 0.31 (15987) SS BOND : bond 0.00651 / 0.31 ( 2) SS BOND : angle 1.52729 / 1.07 ( 4) hydrogen bonds : bond 0.03853 / 2.52 ( 462) hydrogen bonds : angle 4.72233 / 3.33 ( 1356) link_BETA1-4 : bond 0.00112 / 0.06 ( 1) link_BETA1-4 : angle 1.75722 / 1.52 ( 3) link_NAG-ASN : bond 0.00391 / 0.19 ( 3) link_NAG-ASN : angle 1.66494 / 1.34 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 159 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7533 (mm-30) REVERT: A 367 ASN cc_start: 0.7096 (m110) cc_final: 0.6862 (m-40) REVERT: A 369 LYS cc_start: 0.7856 (ptmt) cc_final: 0.6546 (mtpt) REVERT: A 381 THR cc_start: 0.8164 (m) cc_final: 0.7689 (p) REVERT: A 456 ILE cc_start: 0.8365 (tp) cc_final: 0.8086 (mt) REVERT: A 511 PHE cc_start: 0.6563 (t80) cc_final: 0.6345 (t80) REVERT: A 540 THR cc_start: 0.8394 (t) cc_final: 0.7697 (m) REVERT: A 571 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7331 (tp30) REVERT: A 606 ASP cc_start: 0.6668 (t0) cc_final: 0.5883 (m-30) REVERT: A 609 LYS cc_start: 0.7148 (tptm) cc_final: 0.6918 (pttp) REVERT: A 639 GLU cc_start: 0.6446 (tp30) cc_final: 0.6147 (tt0) REVERT: A 664 ASP cc_start: 0.8025 (m-30) cc_final: 0.7714 (m-30) REVERT: A 717 LYS cc_start: 0.6751 (OUTLIER) cc_final: 0.6480 (ptpt) REVERT: A 830 LYS cc_start: 0.8535 (mttt) cc_final: 0.8204 (mtpm) REVERT: A 847 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8171 (mmm) REVERT: A 882 GLU cc_start: 0.6385 (tm-30) cc_final: 0.6027 (tm-30) REVERT: A 994 LYS cc_start: 0.8202 (tmtt) cc_final: 0.7613 (ttmt) REVERT: A 1066 GLN cc_start: 0.7777 (pt0) cc_final: 0.7192 (mt0) REVERT: A 1174 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8185 (mm) REVERT: A 1230 TYR cc_start: 0.7745 (m-80) cc_final: 0.7443 (m-80) REVERT: A 1231 GLU cc_start: 0.6557 (tt0) cc_final: 0.5529 (tm-30) REVERT: A 1241 MET cc_start: 0.5015 (mmm) cc_final: 0.4633 (mtt) REVERT: A 1269 MET cc_start: 0.6509 (OUTLIER) cc_final: 0.5725 (tpt) REVERT: A 1286 GLU cc_start: 0.6824 (pt0) cc_final: 0.5898 (tp30) REVERT: E 73 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8606 (tp) REVERT: E 86 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.7971 (p) REVERT: E 95 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8170 (ptmt) REVERT: E 147 TYR cc_start: 0.8784 (m-80) cc_final: 0.8560 (m-80) REVERT: E 171 ASP cc_start: 0.8018 (m-30) cc_final: 0.7679 (m-30) REVERT: E 193 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.8023 (mt) REVERT: E 247 TRP cc_start: 0.7125 (OUTLIER) cc_final: 0.6307 (p-90) REVERT: E 248 MET cc_start: 0.8416 (mmm) cc_final: 0.8140 (mmm) REVERT: E 268 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7547 (mp0) outliers start: 53 outliers final: 32 residues processed: 198 average time/residue: 0.4896 time to fit residues: 106.6668 Evaluate side-chains 197 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 717 LYS Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1070 SER Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1269 MET Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 247 TRP Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 325 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [26, 139, 64, 109, 47, 97, 81, 93, 95, 3, 134] chunk 26 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 95 optimal weight: 0.0770 chunk 3 optimal weight: 0.5980 chunk 134 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 GLN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1019 ASN A1026 GLN ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.178562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.143554 restraints weight = 12202.810| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.10 r_work: 0.3400 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11807 Z= 0.133 Angle : 0.599 7.837 16003 Z= 0.309 Chirality : 0.044 0.159 1811 Planarity : 0.004 0.046 2010 Dihedral : 5.066 31.199 1543 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.96 % Allowed : 19.18 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.22), residues: 1421 helix: 0.07 (0.22), residues: 599 sheet: -1.08 (0.38), residues: 176 loop : -1.84 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 702 TYR 0.015 0.002 TYR A 913 PHE 0.016 0.001 PHE E 317 TRP 0.029 0.001 TRP E 247 HIS 0.003 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (11801) covalent geometry : angle 0.59666 / 0.31 (15987) SS BOND : bond 0.00642 / 0.31 ( 2) SS BOND : angle 1.50449 / 1.06 ( 4) hydrogen bonds : bond 0.03817 / 2.50 ( 462) hydrogen bonds : angle 4.70776 / 3.32 ( 1356) link_BETA1-4 : bond 0.00069 / 0.04 ( 1) link_BETA1-4 : angle 1.68687 / 1.44 ( 3) link_NAG-ASN : bond 0.00396 / 0.19 ( 3) link_NAG-ASN : angle 1.64937 / 1.32 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 ILE cc_start: 0.8742 (mt) cc_final: 0.8498 (mt) REVERT: A 329 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7705 (mm-30) REVERT: A 367 ASN cc_start: 0.7165 (m110) cc_final: 0.6932 (m-40) REVERT: A 369 LYS cc_start: 0.7919 (ptmt) cc_final: 0.6612 (mtpt) REVERT: A 381 THR cc_start: 0.8172 (m) cc_final: 0.7736 (p) REVERT: A 456 ILE cc_start: 0.8383 (tp) cc_final: 0.8100 (mt) REVERT: A 540 THR cc_start: 0.8420 (t) cc_final: 0.7734 (m) REVERT: A 571 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7464 (tp30) REVERT: A 606 ASP cc_start: 0.6719 (t0) cc_final: 0.5946 (m-30) REVERT: A 609 LYS cc_start: 0.7162 (tptm) cc_final: 0.6932 (pttp) REVERT: A 639 GLU cc_start: 0.6486 (tp30) cc_final: 0.6187 (tt0) REVERT: A 664 ASP cc_start: 0.8049 (m-30) cc_final: 0.7727 (m-30) REVERT: A 830 LYS cc_start: 0.8533 (mttt) cc_final: 0.8239 (mtpm) REVERT: A 847 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8228 (mmm) REVERT: A 882 GLU cc_start: 0.6410 (tm-30) cc_final: 0.6067 (tm-30) REVERT: A 994 LYS cc_start: 0.8211 (tmtt) cc_final: 0.7652 (ttmt) REVERT: A 1050 ASN cc_start: 0.7226 (p0) cc_final: 0.6983 (m-40) REVERT: A 1066 GLN cc_start: 0.7808 (pt0) cc_final: 0.7245 (mt0) REVERT: A 1174 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8199 (mm) REVERT: A 1230 TYR cc_start: 0.7722 (m-80) cc_final: 0.7393 (m-80) REVERT: A 1231 GLU cc_start: 0.6598 (tt0) cc_final: 0.5608 (tm-30) REVERT: A 1241 MET cc_start: 0.5178 (mmm) cc_final: 0.4728 (mtt) REVERT: A 1269 MET cc_start: 0.6509 (OUTLIER) cc_final: 0.5737 (tpt) REVERT: E 73 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8597 (tp) REVERT: E 86 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.8006 (p) REVERT: E 95 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8217 (ptmt) REVERT: E 171 ASP cc_start: 0.8008 (m-30) cc_final: 0.7694 (m-30) REVERT: E 247 TRP cc_start: 0.7042 (OUTLIER) cc_final: 0.6161 (p-90) REVERT: E 248 MET cc_start: 0.8416 (mmm) cc_final: 0.8136 (mmm) REVERT: E 268 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7543 (mp0) outliers start: 50 outliers final: 34 residues processed: 196 average time/residue: 0.5223 time to fit residues: 112.4126 Evaluate side-chains 197 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1070 SER Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1269 MET Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 247 TRP Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [45, 109, 108, 121, 141, 59, 128, 75, 114, 106, 66] chunk 45 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 121 optimal weight: 0.3980 chunk 141 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1019 ASN ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.177421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.142281 restraints weight = 12182.811| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.13 r_work: 0.3404 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11807 Z= 0.152 Angle : 0.617 8.176 16003 Z= 0.319 Chirality : 0.045 0.166 1811 Planarity : 0.004 0.047 2010 Dihedral : 5.105 31.956 1543 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.88 % Allowed : 19.49 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.22), residues: 1421 helix: 0.08 (0.21), residues: 599 sheet: -1.16 (0.39), residues: 169 loop : -1.79 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 702 TYR 0.016 0.002 TYR A 913 PHE 0.016 0.002 PHE E 317 TRP 0.030 0.002 TRP E 247 HIS 0.004 0.001 HIS A1198 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (11801) covalent geometry : angle 0.61465 / 0.32 (15987) SS BOND : bond 0.00706 / 0.34 ( 2) SS BOND : angle 1.68840 / 1.19 ( 4) hydrogen bonds : bond 0.03899 / 2.55 ( 462) hydrogen bonds : angle 4.71657 / 3.33 ( 1356) link_BETA1-4 : bond 0.00093 / 0.05 ( 1) link_BETA1-4 : angle 1.76539 / 1.55 ( 3) link_NAG-ASN : bond 0.00392 / 0.19 ( 3) link_NAG-ASN : angle 1.70871 / 1.38 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4700.03 seconds wall clock time: 80 minutes 52.61 seconds (4852.61 seconds total)