Starting phenix.real_space_refine on Tue Jul 29 17:34:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6psy_20468/07_2025/6psy_20468.cif Found real_map, /net/cci-nas-00/data/ceres_data/6psy_20468/07_2025/6psy_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6psy_20468/07_2025/6psy_20468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6psy_20468/07_2025/6psy_20468.map" model { file = "/net/cci-nas-00/data/ceres_data/6psy_20468/07_2025/6psy_20468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6psy_20468/07_2025/6psy_20468.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.26, per 1000 atoms: 0.63 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: 2.88 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.81 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: 4.45 Time building geometry restraints manager: 3.45 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: 6575 15.37 - 30.74: 390 30.74 - 46.11: 106 46.11 - 61.48: 8 61.48 - 76.85: 10 Dihedral angle restraints: 7089 sinusoidal: 2904 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 7086 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.810 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 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 : 11.326 76.847 4385 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.87 (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 TRP 0.042 0.004 TRP E 247 HIS 0.012 0.002 HIS A1104 PHE 0.038 0.004 PHE E 311 TYR 0.055 0.004 TYR E 336 ARG 0.015 0.001 ARG E 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00657 ( 3) link_NAG-ASN : angle 2.57339 ( 9) link_BETA1-4 : bond 0.00273 ( 1) link_BETA1-4 : angle 1.39259 ( 3) hydrogen bonds : bond 0.17239 ( 462) hydrogen bonds : angle 10.59282 ( 1356) SS BOND : bond 0.01261 ( 2) SS BOND : angle 3.16789 ( 4) covalent geometry : bond 0.00673 (11801) covalent geometry : angle 1.07853 (15987) *********************** 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 : 1.239 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: 0.7313 (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: 0.7271 (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: 1.1360 time to fit residues: 408.6956 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 : 1.402 ------------------------------------------------------------------------------- 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: chunk 119 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 20.0000 chunk 111 optimal weight: 0.4980 chunk 43 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 82 optimal weight: 0.0670 chunk 128 optimal weight: 0.7980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4084 r_free = 0.4084 target = 0.186124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.151358 restraints weight = 12100.265| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.87 r_work: 0.3538 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 11807 Z= 0.158 Angle : 0.682 9.833 16003 Z= 0.357 Chirality : 0.046 0.182 1811 Planarity : 0.005 0.049 2010 Dihedral : 6.449 48.791 1633 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.25 % Allowed : 13.55 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.19), residues: 1421 helix: -2.06 (0.18), residues: 589 sheet: -1.97 (0.36), residues: 187 loop : -2.54 (0.21), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 247 HIS 0.007 0.001 HIS A 745 PHE 0.031 0.002 PHE A 709 TYR 0.018 0.002 TYR E 336 ARG 0.007 0.001 ARG A 437 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 3) link_NAG-ASN : angle 1.85794 ( 9) link_BETA1-4 : bond 0.00001 ( 1) link_BETA1-4 : angle 1.65263 ( 3) hydrogen bonds : bond 0.04554 ( 462) hydrogen bonds : angle 6.14859 ( 1356) SS BOND : bond 0.00850 ( 2) SS BOND : angle 1.89649 ( 4) covalent geometry : bond 0.00369 (11801) covalent geometry : angle 0.67978 (15987) *********************** 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: 41 poor density : 214 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ARG cc_start: 0.7311 (mtp85) cc_final: 0.7108 (mtm110) REVERT: A 248 TYR cc_start: 0.7932 (m-80) cc_final: 0.7653 (m-80) REVERT: A 323 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6970 (mt) REVERT: A 329 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7008 (mt-10) REVERT: A 369 LYS cc_start: 0.7960 (ptmt) cc_final: 0.7474 (ptmm) REVERT: A 381 THR cc_start: 0.8195 (m) cc_final: 0.7716 (p) REVERT: A 386 MET cc_start: 0.8254 (ttm) cc_final: 0.7998 (mtp) REVERT: A 456 ILE cc_start: 0.8478 (tp) cc_final: 0.8193 (mm) REVERT: A 606 ASP cc_start: 0.6791 (t0) cc_final: 0.5915 (m-30) REVERT: A 609 LYS cc_start: 0.7177 (tptm) cc_final: 0.6888 (ttpp) REVERT: A 623 ILE cc_start: 0.7456 (pt) cc_final: 0.7197 (mt) REVERT: A 625 ASP cc_start: 0.7492 (m-30) cc_final: 0.7195 (m-30) REVERT: A 664 ASP cc_start: 0.7897 (m-30) cc_final: 0.7593 (m-30) REVERT: A 670 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6889 (pp) REVERT: A 730 ARG cc_start: 0.7633 (ptp90) cc_final: 0.7408 (ptp-110) REVERT: A 830 LYS cc_start: 0.8409 (mttt) cc_final: 0.8132 (mtpm) REVERT: A 898 ASP cc_start: 0.8229 (m-30) cc_final: 0.7808 (t70) REVERT: A 911 GLU cc_start: 0.6347 (tt0) cc_final: 0.5996 (tt0) REVERT: A 977 MET cc_start: 0.5726 (tpp) cc_final: 0.5509 (tpp) REVERT: A 994 LYS cc_start: 0.8275 (tmtt) cc_final: 0.7761 (ttmt) REVERT: A 1066 GLN cc_start: 0.7783 (pt0) cc_final: 0.7356 (mt0) REVERT: A 1159 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7567 (tttt) REVERT: A 1230 TYR cc_start: 0.7547 (m-80) cc_final: 0.7262 (m-80) REVERT: A 1231 GLU cc_start: 0.6257 (tt0) cc_final: 0.5421 (tm-30) REVERT: A 1286 GLU cc_start: 0.6694 (pt0) cc_final: 0.6119 (tp30) REVERT: E 29 ARG cc_start: 0.7791 (tpp80) cc_final: 0.7504 (mmt180) REVERT: E 86 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.7796 (p) REVERT: E 110 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8623 (mt0) REVERT: E 152 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7952 (ttm-80) REVERT: E 171 ASP cc_start: 0.7839 (m-30) cc_final: 0.7512 (m-30) REVERT: E 209 ILE cc_start: 0.7462 (pp) cc_final: 0.7051 (pp) REVERT: E 218 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8267 (t) REVERT: E 268 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7631 (mt-10) REVERT: E 300 MET cc_start: 0.8386 (tpt) cc_final: 0.8162 (tpp) outliers start: 41 outliers final: 16 residues processed: 233 average time/residue: 1.0962 time to fit residues: 280.4319 Evaluate side-chains 192 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 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 936 LEU Chi-restraints excluded: chain A residue 1068 VAL 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 218 THR Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 308 ILE 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: chunk 58 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 0.0470 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 GLN 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 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.183709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.147514 restraints weight = 12261.753| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.08 r_work: 0.3486 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11807 Z= 0.152 Angle : 0.645 10.711 16003 Z= 0.334 Chirality : 0.046 0.237 1811 Planarity : 0.004 0.044 2010 Dihedral : 5.970 51.580 1627 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.99 % Allowed : 14.26 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.20), residues: 1421 helix: -1.29 (0.20), residues: 587 sheet: -1.55 (0.37), residues: 179 loop : -2.35 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 247 HIS 0.005 0.001 HIS A 745 PHE 0.020 0.002 PHE E 311 TYR 0.019 0.002 TYR E 336 ARG 0.005 0.000 ARG A 437 Details of bonding type rmsd link_NAG-ASN : bond 0.00842 ( 3) link_NAG-ASN : angle 1.96740 ( 9) link_BETA1-4 : bond 0.00085 ( 1) link_BETA1-4 : angle 1.73070 ( 3) hydrogen bonds : bond 0.04233 ( 462) hydrogen bonds : angle 5.44081 ( 1356) SS BOND : bond 0.00726 ( 2) SS BOND : angle 1.68365 ( 4) covalent geometry : bond 0.00350 (11801) covalent geometry : angle 0.64223 (15987) *********************** 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 244 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 181 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 TYR cc_start: 0.8064 (m-80) cc_final: 0.7822 (m-80) REVERT: A 297 LYS cc_start: 0.7734 (mttm) cc_final: 0.7359 (mtpt) REVERT: A 323 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7211 (mt) REVERT: A 329 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7174 (mt-10) REVERT: A 369 LYS cc_start: 0.7893 (ptmt) cc_final: 0.7525 (ptmm) REVERT: A 373 GLU cc_start: 0.7755 (tt0) cc_final: 0.7479 (tt0) REVERT: A 380 TYR cc_start: 0.8396 (m-10) cc_final: 0.8173 (m-10) REVERT: A 381 THR cc_start: 0.8173 (m) cc_final: 0.7721 (p) REVERT: A 386 MET cc_start: 0.8209 (ttm) cc_final: 0.7965 (mtp) REVERT: A 456 ILE cc_start: 0.8469 (tp) cc_final: 0.8216 (mm) REVERT: A 606 ASP cc_start: 0.6864 (t0) cc_final: 0.6084 (m-30) REVERT: A 609 LYS cc_start: 0.7213 (tptm) cc_final: 0.6918 (ttpp) REVERT: A 664 ASP cc_start: 0.8085 (m-30) cc_final: 0.7723 (m-30) REVERT: A 670 ILE cc_start: 0.7197 (OUTLIER) cc_final: 0.6983 (pt) REVERT: A 830 LYS cc_start: 0.8528 (mttt) cc_final: 0.8229 (mtpm) REVERT: A 882 GLU cc_start: 0.6183 (tm-30) cc_final: 0.5972 (tm-30) REVERT: A 898 ASP cc_start: 0.8276 (m-30) cc_final: 0.7821 (t70) REVERT: A 911 GLU cc_start: 0.6662 (tt0) cc_final: 0.6456 (tt0) REVERT: A 977 MET cc_start: 0.5837 (tpp) cc_final: 0.5367 (tpp) REVERT: A 994 LYS cc_start: 0.8178 (tmtt) cc_final: 0.7629 (ttmt) REVERT: A 1066 GLN cc_start: 0.7686 (pt0) cc_final: 0.7276 (mt0) REVERT: A 1159 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7659 (tttt) REVERT: A 1230 TYR cc_start: 0.7666 (m-80) cc_final: 0.7244 (m-80) REVERT: A 1231 GLU cc_start: 0.6428 (tt0) cc_final: 0.5546 (tm-30) REVERT: A 1286 GLU cc_start: 0.6861 (pt0) cc_final: 0.6084 (tp30) REVERT: E 86 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.7858 (p) REVERT: E 110 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8582 (mt0) REVERT: E 134 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7621 (mmtp) REVERT: E 152 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7968 (ttm-80) REVERT: E 171 ASP cc_start: 0.7907 (m-30) cc_final: 0.7561 (m-30) REVERT: E 193 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8099 (mp) REVERT: E 218 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8385 (t) REVERT: E 247 TRP cc_start: 0.7404 (OUTLIER) cc_final: 0.6466 (p-90) outliers start: 63 outliers final: 21 residues processed: 218 average time/residue: 0.9598 time to fit residues: 231.8780 Evaluate side-chains 195 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 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 670 ILE Chi-restraints excluded: chain A residue 706 SER 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 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 1159 LYS 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 134 LYS 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 193 ILE Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 247 TRP Chi-restraints excluded: chain E residue 317 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 72 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 ASN A 878 ASN A1019 ASN ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.181103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.146028 restraints weight = 12223.875| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.17 r_work: 0.3430 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11807 Z= 0.155 Angle : 0.622 8.522 16003 Z= 0.323 Chirality : 0.046 0.212 1811 Planarity : 0.004 0.045 2010 Dihedral : 5.766 55.126 1627 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 5.23 % Allowed : 15.21 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.21), residues: 1421 helix: -0.69 (0.20), residues: 588 sheet: -1.57 (0.36), residues: 192 loop : -2.06 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 247 HIS 0.004 0.001 HIS A 476 PHE 0.018 0.002 PHE E 311 TYR 0.020 0.002 TYR E 147 ARG 0.005 0.000 ARG A 437 Details of bonding type rmsd link_NAG-ASN : bond 0.00650 ( 3) link_NAG-ASN : angle 1.87680 ( 9) link_BETA1-4 : bond 0.00067 ( 1) link_BETA1-4 : angle 1.84431 ( 3) hydrogen bonds : bond 0.04078 ( 462) hydrogen bonds : angle 4.98718 ( 1356) SS BOND : bond 0.00769 ( 2) SS BOND : angle 1.78421 ( 4) covalent geometry : bond 0.00363 (11801) covalent geometry : angle 0.61989 (15987) *********************** 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 245 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 179 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7959 (tt0) REVERT: A 248 TYR cc_start: 0.8332 (m-80) cc_final: 0.8100 (m-80) REVERT: A 297 LYS cc_start: 0.7785 (mttm) cc_final: 0.7421 (mtpt) REVERT: A 323 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.6947 (mt) REVERT: A 329 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7422 (mt-10) REVERT: A 369 LYS cc_start: 0.7892 (ptmt) cc_final: 0.7526 (ptmm) REVERT: A 373 GLU cc_start: 0.7687 (tt0) cc_final: 0.7434 (tt0) REVERT: A 381 THR cc_start: 0.8194 (m) cc_final: 0.7735 (p) REVERT: A 442 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7604 (mtpt) REVERT: A 456 ILE cc_start: 0.8476 (tp) cc_final: 0.8186 (mm) REVERT: A 511 PHE cc_start: 0.6617 (t80) cc_final: 0.6279 (t80) REVERT: A 606 ASP cc_start: 0.6602 (t0) cc_final: 0.5721 (m-30) REVERT: A 609 LYS cc_start: 0.7032 (tptm) cc_final: 0.6763 (ttpp) REVERT: A 664 ASP cc_start: 0.8077 (m-30) cc_final: 0.7708 (m-30) REVERT: A 830 LYS cc_start: 0.8616 (mttt) cc_final: 0.8331 (mtpm) REVERT: A 847 MET cc_start: 0.8389 (tpp) cc_final: 0.8161 (mmm) REVERT: A 882 GLU cc_start: 0.6263 (tm-30) cc_final: 0.6050 (tm-30) REVERT: A 898 ASP cc_start: 0.8166 (m-30) cc_final: 0.7769 (t70) REVERT: A 932 LEU cc_start: 0.7500 (tp) cc_final: 0.7248 (tt) REVERT: A 977 MET cc_start: 0.5830 (tpp) cc_final: 0.5629 (tpp) REVERT: A 994 LYS cc_start: 0.8197 (tmtt) cc_final: 0.7661 (ttmt) REVERT: A 1066 GLN cc_start: 0.7780 (pt0) cc_final: 0.7261 (mt0) REVERT: A 1159 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7616 (tttt) REVERT: A 1230 TYR cc_start: 0.7619 (m-80) cc_final: 0.7197 (m-80) REVERT: A 1231 GLU cc_start: 0.6502 (tt0) cc_final: 0.5572 (tm-30) REVERT: A 1269 MET cc_start: 0.6665 (OUTLIER) cc_final: 0.5991 (tpt) REVERT: A 1286 GLU cc_start: 0.6874 (pt0) cc_final: 0.6009 (tp30) REVERT: E 86 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7930 (p) REVERT: E 95 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7988 (ptmt) REVERT: E 106 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7109 (mt-10) REVERT: E 110 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8670 (mt0) REVERT: E 152 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.8015 (ttm-80) REVERT: E 154 VAL cc_start: 0.8709 (m) cc_final: 0.8378 (t) REVERT: E 171 ASP cc_start: 0.7915 (m-30) cc_final: 0.7633 (m-30) REVERT: E 193 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8077 (mp) REVERT: E 218 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8389 (t) REVERT: E 247 TRP cc_start: 0.7388 (OUTLIER) cc_final: 0.6459 (p-90) REVERT: E 268 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7605 (mp0) outliers start: 66 outliers final: 28 residues processed: 219 average time/residue: 1.7293 time to fit residues: 416.9729 Evaluate side-chains 206 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 310 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 442 LYS 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 679 VAL Chi-restraints excluded: chain A residue 706 SER 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 967 VAL Chi-restraints excluded: chain A residue 1019 ASN 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 1269 MET 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 152 ARG Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 193 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 27 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 136 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 131 optimal weight: 0.4980 chunk 125 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN A 699 ASN A 963 GLN A1038 GLN A1131 HIS E 246 ASN E 299 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.181136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.146123 restraints weight = 12247.527| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.21 r_work: 0.3437 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11807 Z= 0.142 Angle : 0.606 8.120 16003 Z= 0.314 Chirality : 0.045 0.205 1811 Planarity : 0.004 0.045 2010 Dihedral : 5.619 55.508 1627 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.60 % Allowed : 17.12 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.22), residues: 1421 helix: -0.35 (0.21), residues: 586 sheet: -1.47 (0.36), residues: 192 loop : -1.98 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 247 HIS 0.004 0.001 HIS A1198 PHE 0.016 0.001 PHE E 317 TYR 0.017 0.002 TYR E 147 ARG 0.004 0.000 ARG E 29 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 3) link_NAG-ASN : angle 1.82690 ( 9) link_BETA1-4 : bond 0.00031 ( 1) link_BETA1-4 : angle 1.76952 ( 3) hydrogen bonds : bond 0.03951 ( 462) hydrogen bonds : angle 4.85422 ( 1356) SS BOND : bond 0.00716 ( 2) SS BOND : angle 1.68677 ( 4) covalent geometry : bond 0.00329 (11801) covalent geometry : angle 0.60398 (15987) *********************** 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 224 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 166 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7955 (tt0) REVERT: A 297 LYS cc_start: 0.7781 (mttm) cc_final: 0.7390 (mtpt) REVERT: A 323 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6968 (mt) REVERT: A 329 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7427 (mt-10) REVERT: A 369 LYS cc_start: 0.7970 (ptmt) cc_final: 0.7259 (pptt) REVERT: A 373 GLU cc_start: 0.7588 (tt0) cc_final: 0.7376 (tt0) REVERT: A 381 THR cc_start: 0.8178 (m) cc_final: 0.7721 (p) REVERT: A 456 ILE cc_start: 0.8453 (tp) cc_final: 0.8220 (mm) REVERT: A 511 PHE cc_start: 0.6709 (t80) cc_final: 0.6381 (t80) REVERT: A 606 ASP cc_start: 0.6599 (t0) cc_final: 0.5851 (m-30) REVERT: A 664 ASP cc_start: 0.8125 (m-30) cc_final: 0.7751 (m-30) REVERT: A 830 LYS cc_start: 0.8635 (mttt) cc_final: 0.8358 (mtpm) REVERT: A 847 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8155 (mmm) REVERT: A 882 GLU cc_start: 0.6295 (tm-30) cc_final: 0.6047 (tm-30) REVERT: A 898 ASP cc_start: 0.8102 (m-30) cc_final: 0.7743 (t70) REVERT: A 932 LEU cc_start: 0.7542 (tp) cc_final: 0.7306 (tt) REVERT: A 994 LYS cc_start: 0.8237 (tmtt) cc_final: 0.7695 (ttmt) REVERT: A 1046 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.6367 (mtm) REVERT: A 1066 GLN cc_start: 0.7599 (pt0) cc_final: 0.7291 (mt0) REVERT: A 1159 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7663 (tttt) REVERT: A 1230 TYR cc_start: 0.7658 (m-80) cc_final: 0.7258 (m-80) REVERT: A 1231 GLU cc_start: 0.6519 (tt0) cc_final: 0.5577 (tm-30) REVERT: A 1269 MET cc_start: 0.6627 (OUTLIER) cc_final: 0.5981 (tpt) REVERT: A 1286 GLU cc_start: 0.6887 (pt0) cc_final: 0.6065 (tp30) REVERT: E 86 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7855 (p) REVERT: E 95 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8107 (ptmt) REVERT: E 152 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.8014 (ttm-80) REVERT: E 154 VAL cc_start: 0.8686 (m) cc_final: 0.8377 (t) REVERT: E 171 ASP cc_start: 0.7924 (m-30) cc_final: 0.7636 (m-30) REVERT: E 193 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8032 (mp) REVERT: E 218 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8362 (t) REVERT: E 247 TRP cc_start: 0.7304 (OUTLIER) cc_final: 0.6376 (p-90) REVERT: E 268 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7646 (mp0) outliers start: 58 outliers final: 28 residues processed: 203 average time/residue: 1.0646 time to fit residues: 237.2896 Evaluate side-chains 199 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 323 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 335 GLU 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 706 SER Chi-restraints excluded: chain A residue 717 LYS Chi-restraints excluded: chain A residue 840 GLU 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 1068 VAL Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1159 LYS Chi-restraints excluded: chain A residue 1269 MET 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 137 ILE Chi-restraints excluded: chain E residue 152 ARG 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 193 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 105 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN A 699 ASN A1236 HIS A1296 GLN E 155 GLN E 246 ASN E 299 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.175860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.139982 restraints weight = 12241.247| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.28 r_work: 0.3326 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11807 Z= 0.197 Angle : 0.663 10.313 16003 Z= 0.340 Chirality : 0.047 0.211 1811 Planarity : 0.004 0.047 2010 Dihedral : 5.630 44.963 1627 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 5.63 % Allowed : 16.80 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.22), residues: 1421 helix: -0.34 (0.21), residues: 599 sheet: -1.48 (0.36), residues: 195 loop : -1.90 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 247 HIS 0.007 0.001 HIS A1198 PHE 0.022 0.002 PHE E 311 TYR 0.019 0.002 TYR A 913 ARG 0.004 0.001 ARG A1007 Details of bonding type rmsd link_NAG-ASN : bond 0.00624 ( 3) link_NAG-ASN : angle 2.19990 ( 9) link_BETA1-4 : bond 0.00235 ( 1) link_BETA1-4 : angle 2.31688 ( 3) hydrogen bonds : bond 0.04214 ( 462) hydrogen bonds : angle 4.90486 ( 1356) SS BOND : bond 0.00924 ( 2) SS BOND : angle 2.10386 ( 4) covalent geometry : bond 0.00472 (11801) covalent geometry : angle 0.66009 (15987) *********************** 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 243 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 172 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7950 (tt0) REVERT: A 224 LYS cc_start: 0.6520 (tttm) cc_final: 0.6096 (tttp) REVERT: A 323 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7063 (mt) REVERT: A 329 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7467 (mm-30) REVERT: A 369 LYS cc_start: 0.7986 (ptmt) cc_final: 0.6611 (mtpt) REVERT: A 381 THR cc_start: 0.8362 (m) cc_final: 0.7896 (p) REVERT: A 456 ILE cc_start: 0.8432 (tp) cc_final: 0.8142 (mt) REVERT: A 460 LEU cc_start: 0.8083 (mp) cc_final: 0.7862 (mt) REVERT: A 511 PHE cc_start: 0.6720 (t80) cc_final: 0.6286 (t80) REVERT: A 606 ASP cc_start: 0.6629 (t0) cc_final: 0.5868 (m-30) REVERT: A 664 ASP cc_start: 0.8037 (m-30) cc_final: 0.7676 (m-30) REVERT: A 740 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: A 809 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7511 (pt) REVERT: A 830 LYS cc_start: 0.8583 (mttt) cc_final: 0.8302 (mtpm) REVERT: A 932 LEU cc_start: 0.7704 (tp) cc_final: 0.7449 (tt) REVERT: A 994 LYS cc_start: 0.8202 (tmtt) cc_final: 0.7670 (ttmt) REVERT: A 1046 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.6738 (mtm) REVERT: A 1066 GLN cc_start: 0.7789 (pt0) cc_final: 0.7347 (mt0) REVERT: A 1159 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7598 (tttt) REVERT: A 1174 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8287 (mm) REVERT: A 1230 TYR cc_start: 0.7571 (m-80) cc_final: 0.7266 (m-80) REVERT: A 1231 GLU cc_start: 0.6684 (tt0) cc_final: 0.5729 (tm-30) REVERT: A 1286 GLU cc_start: 0.6993 (pt0) cc_final: 0.6181 (tp30) REVERT: E 86 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.7974 (p) REVERT: E 95 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8081 (ptmt) REVERT: E 147 TYR cc_start: 0.8875 (m-80) cc_final: 0.8619 (m-80) REVERT: E 152 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8043 (ttm-80) REVERT: E 154 VAL cc_start: 0.8730 (m) cc_final: 0.8457 (t) REVERT: E 171 ASP cc_start: 0.8008 (m-30) cc_final: 0.7692 (m-30) REVERT: E 247 TRP cc_start: 0.7385 (OUTLIER) cc_final: 0.6859 (p-90) REVERT: E 268 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: E 325 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7903 (pp) outliers start: 71 outliers final: 31 residues processed: 221 average time/residue: 1.0770 time to fit residues: 261.3458 Evaluate side-chains 203 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 467 VAL 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 740 GLU Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 809 ILE 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 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 137 ILE Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 159 THR 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: chunk 55 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 126 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 ASN E 299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.177411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141530 restraints weight = 12314.281| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.25 r_work: 0.3380 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11807 Z= 0.156 Angle : 0.640 8.599 16003 Z= 0.330 Chirality : 0.046 0.210 1811 Planarity : 0.004 0.046 2010 Dihedral : 5.648 57.544 1627 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.28 % Allowed : 18.23 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.22), residues: 1421 helix: -0.12 (0.21), residues: 593 sheet: -1.62 (0.36), residues: 195 loop : -1.88 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 247 HIS 0.004 0.001 HIS A1104 PHE 0.017 0.002 PHE E 317 TYR 0.014 0.002 TYR E 236 ARG 0.004 0.000 ARG A 672 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 3) link_NAG-ASN : angle 2.05787 ( 9) link_BETA1-4 : bond 0.00127 ( 1) link_BETA1-4 : angle 1.88269 ( 3) hydrogen bonds : bond 0.04012 ( 462) hydrogen bonds : angle 4.82556 ( 1356) SS BOND : bond 0.00749 ( 2) SS BOND : angle 1.73364 ( 4) covalent geometry : bond 0.00369 (11801) covalent geometry : angle 0.63691 (15987) *********************** 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 221 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 167 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7878 (tt0) REVERT: A 323 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7052 (mt) REVERT: A 329 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7488 (mm-30) REVERT: A 369 LYS cc_start: 0.7930 (ptmt) cc_final: 0.6570 (mtpt) REVERT: A 381 THR cc_start: 0.8283 (m) cc_final: 0.7807 (p) REVERT: A 442 LYS cc_start: 0.7961 (mtpt) cc_final: 0.7662 (mppt) REVERT: A 456 ILE cc_start: 0.8405 (tp) cc_final: 0.8111 (mt) REVERT: A 460 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7803 (mt) REVERT: A 511 PHE cc_start: 0.6755 (t80) cc_final: 0.6350 (t80) REVERT: A 606 ASP cc_start: 0.6655 (t0) cc_final: 0.6048 (m-30) REVERT: A 664 ASP cc_start: 0.8038 (m-30) cc_final: 0.7683 (m-30) REVERT: A 809 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7414 (pt) REVERT: A 830 LYS cc_start: 0.8589 (mttt) cc_final: 0.8313 (mtpm) REVERT: A 882 GLU cc_start: 0.6663 (tm-30) cc_final: 0.6230 (tm-30) REVERT: A 932 LEU cc_start: 0.7720 (tp) cc_final: 0.7470 (tt) REVERT: A 994 LYS cc_start: 0.8204 (tmtt) cc_final: 0.7667 (ttmt) REVERT: A 1046 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.6609 (mtm) REVERT: A 1066 GLN cc_start: 0.7807 (pt0) cc_final: 0.7326 (mt0) REVERT: A 1174 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8234 (mm) REVERT: A 1230 TYR cc_start: 0.7776 (m-80) cc_final: 0.7483 (m-80) REVERT: A 1231 GLU cc_start: 0.6605 (tt0) cc_final: 0.5596 (tm-30) REVERT: A 1286 GLU cc_start: 0.6983 (pt0) cc_final: 0.6177 (tp30) REVERT: E 73 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8602 (tp) REVERT: E 86 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8025 (p) REVERT: E 95 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8139 (ptmt) REVERT: E 147 TYR cc_start: 0.8815 (m-80) cc_final: 0.8571 (m-80) REVERT: E 152 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.8010 (ttm-80) REVERT: E 154 VAL cc_start: 0.8660 (m) cc_final: 0.8371 (t) REVERT: E 171 ASP cc_start: 0.7964 (m-30) cc_final: 0.7630 (m-30) REVERT: E 247 TRP cc_start: 0.7320 (OUTLIER) cc_final: 0.6662 (p-90) REVERT: E 248 MET cc_start: 0.8448 (mmm) cc_final: 0.8245 (mmm) REVERT: E 268 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: E 325 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7865 (pp) outliers start: 54 outliers final: 30 residues processed: 205 average time/residue: 1.0743 time to fit residues: 241.2574 Evaluate side-chains 201 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 460 LEU 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 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 756 THR Chi-restraints excluded: chain A residue 809 ILE 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 1228 ARG 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 152 ARG Chi-restraints excluded: chain E residue 159 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 134 optimal weight: 0.1980 chunk 77 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN A 699 ASN A1019 ASN E 299 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.178368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.142385 restraints weight = 12229.814| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.20 r_work: 0.3392 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11807 Z= 0.143 Angle : 0.618 7.992 16003 Z= 0.319 Chirality : 0.045 0.270 1811 Planarity : 0.004 0.046 2010 Dihedral : 5.545 59.528 1627 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 4.36 % Allowed : 18.38 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.22), residues: 1421 helix: 0.01 (0.22), residues: 595 sheet: -1.53 (0.36), residues: 195 loop : -1.82 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 247 HIS 0.004 0.001 HIS A 634 PHE 0.017 0.002 PHE A 709 TYR 0.016 0.002 TYR E 147 ARG 0.003 0.000 ARG A 437 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 3) link_NAG-ASN : angle 1.93185 ( 9) link_BETA1-4 : bond 0.00010 ( 1) link_BETA1-4 : angle 1.78190 ( 3) hydrogen bonds : bond 0.03899 ( 462) hydrogen bonds : angle 4.72102 ( 1356) SS BOND : bond 0.00687 ( 2) SS BOND : angle 1.60916 ( 4) covalent geometry : bond 0.00336 (11801) covalent geometry : angle 0.61576 (15987) *********************** 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 218 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8107 (tm-30) cc_final: 0.7834 (tt0) REVERT: A 329 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7499 (mm-30) REVERT: A 369 LYS cc_start: 0.7855 (ptmt) cc_final: 0.6561 (mtpt) REVERT: A 381 THR cc_start: 0.8163 (m) cc_final: 0.7716 (p) REVERT: A 386 MET cc_start: 0.8229 (ttp) cc_final: 0.8018 (mtp) REVERT: A 442 LYS cc_start: 0.7929 (mtpt) cc_final: 0.7635 (mppt) REVERT: A 456 ILE cc_start: 0.8403 (tp) cc_final: 0.8104 (mt) REVERT: A 460 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7799 (mt) REVERT: A 511 PHE cc_start: 0.6446 (t80) cc_final: 0.6237 (t80) REVERT: A 553 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7975 (mm110) REVERT: A 606 ASP cc_start: 0.6662 (t0) cc_final: 0.5883 (m-30) REVERT: A 664 ASP cc_start: 0.8018 (m-30) cc_final: 0.7677 (m-30) REVERT: A 830 LYS cc_start: 0.8573 (mttt) cc_final: 0.8294 (mtpm) REVERT: A 882 GLU cc_start: 0.6618 (tm-30) cc_final: 0.6250 (tm-30) REVERT: A 932 LEU cc_start: 0.7638 (tp) cc_final: 0.7380 (tt) REVERT: A 994 LYS cc_start: 0.8195 (tmtt) cc_final: 0.7633 (ttmt) REVERT: A 1046 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.6406 (mtm) REVERT: A 1066 GLN cc_start: 0.7753 (pt0) cc_final: 0.7272 (mt0) REVERT: A 1174 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8237 (mm) REVERT: A 1230 TYR cc_start: 0.7705 (m-80) cc_final: 0.7444 (m-80) REVERT: A 1231 GLU cc_start: 0.6553 (tt0) cc_final: 0.5549 (tm-30) REVERT: A 1286 GLU cc_start: 0.6989 (pt0) cc_final: 0.6160 (tp30) REVERT: E 86 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8034 (p) REVERT: E 95 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8148 (ptmt) REVERT: E 154 VAL cc_start: 0.8579 (m) cc_final: 0.8362 (t) REVERT: E 171 ASP cc_start: 0.8008 (m-30) cc_final: 0.7667 (m-30) REVERT: E 247 TRP cc_start: 0.7240 (OUTLIER) cc_final: 0.6475 (p-90) REVERT: E 248 MET cc_start: 0.8464 (mmm) cc_final: 0.8225 (mmm) REVERT: E 268 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7583 (mp0) outliers start: 55 outliers final: 32 residues processed: 200 average time/residue: 1.1235 time to fit residues: 245.7294 Evaluate side-chains 194 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 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 438 THR Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 460 LEU 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 553 GLN 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 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 1228 ARG 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 159 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 14 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 0.0040 chunk 3 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.178572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.142893 restraints weight = 12244.717| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.24 r_work: 0.3398 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11807 Z= 0.140 Angle : 0.616 7.952 16003 Z= 0.317 Chirality : 0.045 0.295 1811 Planarity : 0.004 0.046 2010 Dihedral : 5.530 59.735 1627 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.72 % Allowed : 19.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.22), residues: 1421 helix: 0.06 (0.22), residues: 595 sheet: -1.46 (0.37), residues: 183 loop : -1.80 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 247 HIS 0.004 0.001 HIS A 634 PHE 0.016 0.002 PHE E 317 TYR 0.014 0.002 TYR E 236 ARG 0.003 0.000 ARG A 437 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 3) link_NAG-ASN : angle 1.90180 ( 9) link_BETA1-4 : bond 0.00018 ( 1) link_BETA1-4 : angle 1.76952 ( 3) hydrogen bonds : bond 0.03873 ( 462) hydrogen bonds : angle 4.71755 ( 1356) SS BOND : bond 0.00674 ( 2) SS BOND : angle 1.57585 ( 4) covalent geometry : bond 0.00328 (11801) covalent geometry : angle 0.61356 (15987) *********************** 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 200 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7603 (mm-30) REVERT: A 369 LYS cc_start: 0.7849 (ptmt) cc_final: 0.6547 (mtpt) REVERT: A 381 THR cc_start: 0.8136 (m) cc_final: 0.7693 (p) REVERT: A 442 LYS cc_start: 0.7932 (mtpt) cc_final: 0.7636 (mppt) REVERT: A 456 ILE cc_start: 0.8401 (tp) cc_final: 0.8104 (mt) REVERT: A 460 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7816 (mt) REVERT: A 540 THR cc_start: 0.8390 (t) cc_final: 0.7729 (m) REVERT: A 606 ASP cc_start: 0.6722 (t0) cc_final: 0.5768 (m-30) REVERT: A 639 GLU cc_start: 0.6426 (tp30) cc_final: 0.6127 (tt0) REVERT: A 664 ASP cc_start: 0.8000 (m-30) cc_final: 0.7657 (m-30) REVERT: A 830 LYS cc_start: 0.8563 (mttt) cc_final: 0.8292 (mtpm) REVERT: A 882 GLU cc_start: 0.6619 (tm-30) cc_final: 0.6297 (tm-30) REVERT: A 994 LYS cc_start: 0.8208 (tmtt) cc_final: 0.7645 (ttmt) REVERT: A 1066 GLN cc_start: 0.7772 (pt0) cc_final: 0.7278 (mt0) REVERT: A 1174 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8222 (mm) REVERT: A 1230 TYR cc_start: 0.7741 (m-80) cc_final: 0.7468 (m-80) REVERT: A 1231 GLU cc_start: 0.6583 (tt0) cc_final: 0.5604 (tm-30) REVERT: A 1286 GLU cc_start: 0.6858 (pt0) cc_final: 0.6098 (tp30) REVERT: E 73 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8611 (tp) REVERT: E 86 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.8088 (p) REVERT: E 95 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8159 (ptmt) REVERT: E 152 ARG cc_start: 0.8469 (ttm-80) cc_final: 0.8074 (ttt180) REVERT: E 171 ASP cc_start: 0.8023 (m-30) cc_final: 0.7699 (m-30) REVERT: E 247 TRP cc_start: 0.7191 (OUTLIER) cc_final: 0.6422 (p-90) REVERT: E 248 MET cc_start: 0.8430 (mmm) cc_final: 0.8170 (mmm) REVERT: E 268 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7561 (mp0) outliers start: 47 outliers final: 31 residues processed: 186 average time/residue: 1.0864 time to fit residues: 221.6667 Evaluate side-chains 189 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 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 460 LEU 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 636 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 874 LEU 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 1138 VAL 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 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 159 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 12 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 23 optimal weight: 0.0980 chunk 128 optimal weight: 0.2980 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 88 optimal weight: 0.0770 chunk 107 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN A 699 ASN A 857 ASN A1019 ASN ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.181169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.146050 restraints weight = 12088.730| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.95 r_work: 0.3466 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11807 Z= 0.124 Angle : 0.600 7.817 16003 Z= 0.308 Chirality : 0.044 0.276 1811 Planarity : 0.004 0.046 2010 Dihedral : 5.346 55.725 1627 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.85 % Allowed : 20.60 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.22), residues: 1421 helix: 0.12 (0.22), residues: 601 sheet: -1.40 (0.36), residues: 190 loop : -1.84 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 247 HIS 0.004 0.001 HIS A1104 PHE 0.017 0.001 PHE A 511 TYR 0.017 0.001 TYR E 147 ARG 0.003 0.000 ARG A 437 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 3) link_NAG-ASN : angle 1.76594 ( 9) link_BETA1-4 : bond 0.00113 ( 1) link_BETA1-4 : angle 1.52351 ( 3) hydrogen bonds : bond 0.03716 ( 462) hydrogen bonds : angle 4.65310 ( 1356) SS BOND : bond 0.00589 ( 2) SS BOND : angle 1.33989 ( 4) covalent geometry : bond 0.00284 (11801) covalent geometry : angle 0.59822 (15987) ********************** 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 193 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 LYS cc_start: 0.7935 (ptmt) cc_final: 0.6539 (mtpt) REVERT: A 381 THR cc_start: 0.8069 (m) cc_final: 0.7677 (p) REVERT: A 388 LEU cc_start: 0.5431 (OUTLIER) cc_final: 0.5147 (mt) REVERT: A 442 LYS cc_start: 0.7919 (mtpt) cc_final: 0.7651 (mttp) REVERT: A 456 ILE cc_start: 0.8395 (tp) cc_final: 0.8118 (mt) REVERT: A 460 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7760 (mt) REVERT: A 540 THR cc_start: 0.8349 (t) cc_final: 0.7727 (m) REVERT: A 664 ASP cc_start: 0.8183 (m-30) cc_final: 0.7869 (m-30) REVERT: A 830 LYS cc_start: 0.8528 (mttt) cc_final: 0.8282 (mtpm) REVERT: A 847 MET cc_start: 0.8394 (tpp) cc_final: 0.8020 (mmm) REVERT: A 882 GLU cc_start: 0.6516 (tm-30) cc_final: 0.6249 (tm-30) REVERT: A 994 LYS cc_start: 0.8216 (tmtt) cc_final: 0.7662 (ttmt) REVERT: A 1066 GLN cc_start: 0.7723 (pt0) cc_final: 0.7247 (mt0) REVERT: A 1174 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8183 (mm) REVERT: A 1230 TYR cc_start: 0.7731 (m-80) cc_final: 0.7457 (m-80) REVERT: A 1231 GLU cc_start: 0.6536 (tt0) cc_final: 0.5598 (tm-30) REVERT: E 73 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8600 (tp) REVERT: E 95 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8129 (ptmt) REVERT: E 171 ASP cc_start: 0.8051 (m-30) cc_final: 0.7733 (m-30) REVERT: E 247 TRP cc_start: 0.7065 (OUTLIER) cc_final: 0.6142 (p-90) REVERT: E 248 MET cc_start: 0.8338 (mmm) cc_final: 0.8053 (mmm) REVERT: E 268 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7550 (mp0) outliers start: 36 outliers final: 19 residues processed: 184 average time/residue: 1.1039 time to fit residues: 223.9055 Evaluate side-chains 176 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 388 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 460 LEU 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 636 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 897 ILE 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 1174 ILE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 95 LYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 57 optimal weight: 30.0000 chunk 125 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 140 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN A 641 GLN A1019 ASN A1026 GLN ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.177184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.141266 restraints weight = 12112.749| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.24 r_work: 0.3385 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11807 Z= 0.167 Angle : 0.645 8.720 16003 Z= 0.330 Chirality : 0.046 0.289 1811 Planarity : 0.004 0.047 2010 Dihedral : 5.536 59.417 1627 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.93 % Allowed : 21.00 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.22), residues: 1421 helix: 0.10 (0.22), residues: 596 sheet: -1.30 (0.37), residues: 187 loop : -1.78 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 247 HIS 0.005 0.001 HIS A1198 PHE 0.016 0.002 PHE E 311 TYR 0.028 0.002 TYR E 147 ARG 0.003 0.000 ARG A 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 3) link_NAG-ASN : angle 2.05626 ( 9) link_BETA1-4 : bond 0.00117 ( 1) link_BETA1-4 : angle 1.97130 ( 3) hydrogen bonds : bond 0.04005 ( 462) hydrogen bonds : angle 4.75001 ( 1356) SS BOND : bond 0.00778 ( 2) SS BOND : angle 1.77628 ( 4) covalent geometry : bond 0.00399 (11801) covalent geometry : angle 0.64246 (15987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10917.30 seconds wall clock time: 193 minutes 4.45 seconds (11584.45 seconds total)