Starting phenix.real_space_refine on Thu Jun 12 07:05:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ip2_60755/06_2025/9ip2_60755.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ip2_60755/06_2025/9ip2_60755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ip2_60755/06_2025/9ip2_60755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ip2_60755/06_2025/9ip2_60755.map" model { file = "/net/cci-nas-00/data/ceres_data/9ip2_60755/06_2025/9ip2_60755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ip2_60755/06_2025/9ip2_60755.cif" } resolution = 2.7 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= 0.001 sd= 0.052 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 69 5.16 5 C 8738 2.51 5 N 2311 2.21 5 O 2487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13606 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1363, 11040 Classifications: {'peptide': 1363} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1303} Chain breaks: 6 Chain: "B" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1649 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "C" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 5, 'TRANS': 57} Chain: "D" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 244 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "E" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 201 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8878 SG CYS A1108 32.108 20.473 35.084 1.00 61.94 S ATOM 10710 SG CYS A1376 28.360 21.941 34.231 1.00 83.79 S ATOM 10716 SG CYS A1377 30.727 23.468 36.500 1.00 67.25 S Time building chain proxies: 8.29, per 1000 atoms: 0.61 Number of scatterers: 13606 At special positions: 0 Unit cell: (97.865, 124.246, 125.097, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 69 16.00 O 2487 8.00 N 2311 7.00 C 8738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2801 " pdb="ZN ZN A2801 " - pdb=" SG CYS A1108 " pdb="ZN ZN A2801 " - pdb=" SG CYS A1377 " pdb="ZN ZN A2801 " - pdb=" SG CYS A1376 " 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 9 sheets defined 60.4% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 18 through 28 removed outlier: 4.077A pdb=" N ASP A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 removed outlier: 4.373A pdb=" N ASN A 42 " --> pdb=" O PRO A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 72 through 87 removed outlier: 3.659A pdb=" N ASP A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N HIS A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 95 removed outlier: 4.032A pdb=" N VAL A 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP A 92 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 95 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 122 Processing helix chain 'A' and resid 137 through 143 Processing helix chain 'A' and resid 145 through 165 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 210 through 215 removed outlier: 3.656A pdb=" N ILE A 214 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 237 through 264 Processing helix chain 'A' and resid 272 through 291 Processing helix chain 'A' and resid 293 through 299 removed outlier: 3.844A pdb=" N LEU A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 316 through 319 Processing helix chain 'A' and resid 320 through 341 Processing helix chain 'A' and resid 348 through 361 removed outlier: 4.237A pdb=" N GLN A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 384 through 398 removed outlier: 4.009A pdb=" N LYS A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 427 Processing helix chain 'A' and resid 435 through 438 removed outlier: 3.591A pdb=" N LEU A 438 " --> pdb=" O ASP A 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 435 through 438' Processing helix chain 'A' and resid 439 through 448 removed outlier: 3.591A pdb=" N GLN A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS A 445 " --> pdb=" O TYR A 441 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 466 Processing helix chain 'A' and resid 493 through 501 removed outlier: 3.917A pdb=" N TRP A 497 " --> pdb=" O GLN A 494 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ASP A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER A 499 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL A 500 " --> pdb=" O TRP A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 518 through 524 removed outlier: 3.712A pdb=" N LEU A 524 " --> pdb=" O PRO A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 540 removed outlier: 3.935A pdb=" N ILE A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 549 Proline residue: A 546 - end of helix removed outlier: 3.770A pdb=" N ARG A 549 " --> pdb=" O PRO A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 587 Processing helix chain 'A' and resid 588 through 592 removed outlier: 3.599A pdb=" N PHE A 592 " --> pdb=" O ALA A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 604 through 612 Processing helix chain 'A' and resid 637 through 643 removed outlier: 3.729A pdb=" N ASN A 640 " --> pdb=" O GLU A 637 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU A 641 " --> pdb=" O LYS A 638 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 643 " --> pdb=" O ASN A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 660 removed outlier: 5.832A pdb=" N HIS A 650 " --> pdb=" O GLU A 646 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N PHE A 651 " --> pdb=" O PHE A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 672 Processing helix chain 'A' and resid 691 through 695 removed outlier: 3.582A pdb=" N ARG A 694 " --> pdb=" O GLU A 691 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASN A 695 " --> pdb=" O ASP A 692 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 691 through 695' Processing helix chain 'A' and resid 715 through 735 Processing helix chain 'A' and resid 760 through 785 removed outlier: 3.520A pdb=" N GLU A 769 " --> pdb=" O GLU A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 795 removed outlier: 3.501A pdb=" N THR A 795 " --> pdb=" O PRO A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 823 Processing helix chain 'A' and resid 835 through 853 Processing helix chain 'A' and resid 857 through 878 removed outlier: 3.759A pdb=" N ILE A 863 " --> pdb=" O PRO A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 894 Processing helix chain 'A' and resid 898 through 908 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 930 through 947 removed outlier: 3.571A pdb=" N SER A 934 " --> pdb=" O ASP A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 951 through 957 removed outlier: 3.620A pdb=" N SER A 957 " --> pdb=" O TYR A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 971 removed outlier: 3.635A pdb=" N PHE A 968 " --> pdb=" O ASP A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 981 removed outlier: 3.556A pdb=" N SER A 980 " --> pdb=" O VAL A 977 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS A 981 " --> pdb=" O PRO A 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 977 through 981' Processing helix chain 'A' and resid 983 through 999 removed outlier: 3.816A pdb=" N LEU A 987 " --> pdb=" O ILE A 983 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLN A 989 " --> pdb=" O THR A 985 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N THR A 990 " --> pdb=" O PHE A 986 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 997 " --> pdb=" O GLU A 993 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 999 " --> pdb=" O ILE A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1008 Processing helix chain 'A' and resid 1011 through 1024 removed outlier: 3.539A pdb=" N GLU A1015 " --> pdb=" O GLY A1011 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A1024 " --> pdb=" O CYS A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1039 Processing helix chain 'A' and resid 1041 through 1055 removed outlier: 4.531A pdb=" N GLY A1055 " --> pdb=" O GLY A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1090 Processing helix chain 'A' and resid 1096 through 1104 Processing helix chain 'A' and resid 1108 through 1121 Processing helix chain 'A' and resid 1121 through 1126 Processing helix chain 'A' and resid 1137 through 1141 Processing helix chain 'A' and resid 1150 through 1157 removed outlier: 3.691A pdb=" N GLU A1155 " --> pdb=" O GLU A1151 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN A1156 " --> pdb=" O ASP A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1216 through 1221 removed outlier: 4.160A pdb=" N GLY A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER A1221 " --> pdb=" O PRO A1217 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1216 through 1221' Processing helix chain 'A' and resid 1238 through 1255 Processing helix chain 'A' and resid 1260 through 1270 removed outlier: 4.090A pdb=" N LEU A1264 " --> pdb=" O ASP A1260 " (cutoff:3.500A) Proline residue: A1267 - end of helix Processing helix chain 'A' and resid 1276 through 1282 removed outlier: 3.806A pdb=" N VAL A1280 " --> pdb=" O ASP A1276 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A1281 " --> pdb=" O TYR A1277 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN A1282 " --> pdb=" O GLN A1278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1276 through 1282' Processing helix chain 'A' and resid 1291 through 1301 removed outlier: 4.060A pdb=" N ASN A1297 " --> pdb=" O VAL A1293 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A1298 " --> pdb=" O HIS A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1315 No H-bonds generated for 'chain 'A' and resid 1313 through 1315' Processing helix chain 'A' and resid 1324 through 1328 Processing helix chain 'A' and resid 1342 through 1356 removed outlier: 3.903A pdb=" N ASN A1346 " --> pdb=" O GLN A1342 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A1356 " --> pdb=" O LEU A1352 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 138 removed outlier: 4.090A pdb=" N ILE B 120 " --> pdb=" O THR B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 156 Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 183 through 197 Processing helix chain 'B' and resid 209 through 220 Processing helix chain 'B' and resid 226 through 242 removed outlier: 3.686A pdb=" N ILE B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 258 Processing helix chain 'B' and resid 261 through 273 Processing helix chain 'B' and resid 274 through 277 Processing helix chain 'B' and resid 293 through 298 removed outlier: 4.551A pdb=" N LYS B 298 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 311 Processing helix chain 'C' and resid 111 through 132 removed outlier: 3.595A pdb=" N LYS C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 156 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'D' and resid 108 through 135 removed outlier: 4.275A pdb=" N GLU D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 135 removed outlier: 3.840A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL E 135 " --> pdb=" O TYR E 131 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 69 removed outlier: 5.802A pdb=" N VAL A 232 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU A 68 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL A 234 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 401 through 402 Processing sheet with id=AA3, first strand: chain 'A' and resid 565 through 568 Processing sheet with id=AA4, first strand: chain 'A' and resid 737 through 742 removed outlier: 4.323A pdb=" N LYS A 737 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 801 through 803 Processing sheet with id=AA6, first strand: chain 'A' and resid 1028 through 1030 removed outlier: 6.263A pdb=" N VAL A1029 " --> pdb=" O ILE A1131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1142 through 1149 removed outlier: 6.769A pdb=" N THR A1368 " --> pdb=" O ILE A1147 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL A1367 " --> pdb=" O LEU A1194 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1200 through 1201 removed outlier: 3.846A pdb=" N GLN A1200 " --> pdb=" O ILE A1212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.979A pdb=" N CYS B 315 " --> pdb=" O LEU B 327 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 1926 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: 4.53 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 2799 1.33 - 1.46: 4578 1.46 - 1.60: 6445 1.60 - 1.74: 7 1.74 - 1.87: 100 Bond restraints: 13929 Sorted by residual: bond pdb=" CB LYS A1398 " pdb=" CG LYS A1398 " ideal model delta sigma weight residual 1.520 1.386 0.134 3.00e-02 1.11e+03 1.98e+01 bond pdb=" CG LYS A1263 " pdb=" CD LYS A1263 " ideal model delta sigma weight residual 1.520 1.400 0.120 3.00e-02 1.11e+03 1.59e+01 bond pdb=" CB ASN A 702 " pdb=" CG ASN A 702 " ideal model delta sigma weight residual 1.516 1.423 0.093 2.50e-02 1.60e+03 1.37e+01 bond pdb=" C HIS A 73 " pdb=" O HIS A 73 " ideal model delta sigma weight residual 1.236 1.280 -0.044 1.22e-02 6.72e+03 1.30e+01 bond pdb=" CB ARG A 649 " pdb=" CG ARG A 649 " ideal model delta sigma weight residual 1.520 1.415 0.105 3.00e-02 1.11e+03 1.22e+01 ... (remaining 13924 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.35: 18719 5.35 - 10.70: 134 10.70 - 16.06: 16 16.06 - 21.41: 5 21.41 - 26.76: 4 Bond angle restraints: 18878 Sorted by residual: angle pdb=" C GLN C 161 " pdb=" N PRO C 162 " pdb=" CA PRO C 162 " ideal model delta sigma weight residual 120.45 131.86 -11.41 1.11e+00 8.12e-01 1.06e+02 angle pdb=" CB MET C 113 " pdb=" CG MET C 113 " pdb=" SD MET C 113 " ideal model delta sigma weight residual 112.70 85.94 26.76 3.00e+00 1.11e-01 7.96e+01 angle pdb=" CG LYS A1263 " pdb=" CD LYS A1263 " pdb=" CE LYS A1263 " ideal model delta sigma weight residual 111.30 91.31 19.99 2.30e+00 1.89e-01 7.56e+01 angle pdb=" CG ARG A 26 " pdb=" CD ARG A 26 " pdb=" NE ARG A 26 " ideal model delta sigma weight residual 112.00 92.95 19.05 2.20e+00 2.07e-01 7.50e+01 angle pdb=" CB LEU A1241 " pdb=" CG LEU A1241 " pdb=" CD2 LEU A1241 " ideal model delta sigma weight residual 110.70 86.39 24.31 3.00e+00 1.11e-01 6.57e+01 ... (remaining 18873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 7657 17.92 - 35.84: 593 35.84 - 53.76: 88 53.76 - 71.68: 12 71.68 - 89.60: 12 Dihedral angle restraints: 8362 sinusoidal: 3365 harmonic: 4997 Sorted by residual: dihedral pdb=" C ASN A 624 " pdb=" N ASN A 624 " pdb=" CA ASN A 624 " pdb=" CB ASN A 624 " ideal model delta harmonic sigma weight residual -122.60 -136.11 13.51 0 2.50e+00 1.60e-01 2.92e+01 dihedral pdb=" N ASN A 624 " pdb=" C ASN A 624 " pdb=" CA ASN A 624 " pdb=" CB ASN A 624 " ideal model delta harmonic sigma weight residual 122.80 135.95 -13.15 0 2.50e+00 1.60e-01 2.77e+01 dihedral pdb=" CA ASN A1291 " pdb=" C ASN A1291 " pdb=" N ILE A1292 " pdb=" CA ILE A1292 " ideal model delta harmonic sigma weight residual -180.00 -155.93 -24.07 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 8359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 2009 0.160 - 0.321: 91 0.321 - 0.481: 5 0.481 - 0.641: 1 0.641 - 0.801: 1 Chirality restraints: 2107 Sorted by residual: chirality pdb=" CG LEU A1275 " pdb=" CB LEU A1275 " pdb=" CD1 LEU A1275 " pdb=" CD2 LEU A1275 " both_signs ideal model delta sigma weight residual False -2.59 -1.79 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CA ASN A 624 " pdb=" N ASN A 624 " pdb=" C ASN A 624 " pdb=" CB ASN A 624 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.01e+00 chirality pdb=" CG LEU A 636 " pdb=" CB LEU A 636 " pdb=" CD1 LEU A 636 " pdb=" CD2 LEU A 636 " both_signs ideal model delta sigma weight residual False -2.59 -2.99 0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 2104 not shown) Planarity restraints: 2401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 726 " -0.034 2.00e-02 2.50e+03 6.62e-02 4.39e+01 pdb=" CD GLN A 726 " 0.115 2.00e-02 2.50e+03 pdb=" OE1 GLN A 726 " -0.042 2.00e-02 2.50e+03 pdb=" NE2 GLN A 726 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 949 " -0.028 2.00e-02 2.50e+03 5.89e-02 3.47e+01 pdb=" CD GLU A 949 " 0.102 2.00e-02 2.50e+03 pdb=" OE1 GLU A 949 " -0.039 2.00e-02 2.50e+03 pdb=" OE2 GLU A 949 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 430 " -0.031 2.00e-02 2.50e+03 3.58e-02 2.56e+01 pdb=" CG TYR A 430 " 0.086 2.00e-02 2.50e+03 pdb=" CD1 TYR A 430 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 430 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 TYR A 430 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 430 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 430 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR A 430 " 0.008 2.00e-02 2.50e+03 ... (remaining 2398 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 20 2.35 - 2.98: 6951 2.98 - 3.62: 18276 3.62 - 4.26: 29563 4.26 - 4.90: 51538 Nonbonded interactions: 106348 Sorted by model distance: nonbonded pdb=" OE1 GLU A 539 " pdb=" O LYS A 662 " model vdw 1.708 3.040 nonbonded pdb=" NH1 ARG A1040 " pdb=" OE1 GLU A1246 " model vdw 1.962 3.120 nonbonded pdb=" N GLU A 623 " pdb=" OE1 GLU A 623 " model vdw 2.078 3.120 nonbonded pdb=" OE2 GLU A1140 " pdb="ZN ZN A2801 " model vdw 2.082 2.230 nonbonded pdb=" O ASP A1260 " pdb=" NZ LYS A1263 " model vdw 2.121 3.120 ... (remaining 106343 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 35.180 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.060 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:13.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 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 : 0.012 0.134 13932 Z= 0.552 Angle : 1.442 26.762 18878 Z= 0.786 Chirality : 0.078 0.801 2107 Planarity : 0.008 0.084 2401 Dihedral : 13.141 89.596 5122 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.93 % Favored : 96.01 % Rotamer: Outliers : 0.13 % Allowed : 1.20 % Favored : 98.67 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 1.27 % 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: -0.04 (0.20), residues: 1679 helix: 0.95 (0.18), residues: 861 sheet: 0.78 (0.51), residues: 92 loop : -1.35 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.006 TRP A1253 HIS 0.027 0.005 HIS A 687 PHE 0.057 0.006 PHE A 529 TYR 0.086 0.005 TYR A 430 ARG 0.054 0.002 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.19347 ( 680) hydrogen bonds : angle 6.32314 ( 1926) metal coordination : bond 0.03387 ( 3) covalent geometry : bond 0.01229 (13929) covalent geometry : angle 1.44190 (18878) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 256 time to evaluate : 1.688 Fit side-chains REVERT: A 59 LYS cc_start: 0.8566 (mtmt) cc_final: 0.8347 (mttm) REVERT: A 141 LYS cc_start: 0.8379 (ttpp) cc_final: 0.8040 (ttpt) REVERT: A 217 ARG cc_start: 0.7316 (mpp-170) cc_final: 0.6566 (mmt-90) REVERT: A 349 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7143 (pt0) REVERT: A 436 LEU cc_start: 0.7663 (mm) cc_final: 0.7426 (mm) REVERT: A 443 ARG cc_start: 0.8130 (ttt180) cc_final: 0.7809 (ttm-80) REVERT: A 459 GLN cc_start: 0.8444 (tt0) cc_final: 0.7944 (tp40) REVERT: A 536 GLU cc_start: 0.8082 (tp30) cc_final: 0.7620 (mm-30) REVERT: A 572 ARG cc_start: 0.7607 (mtp85) cc_final: 0.7220 (mtp180) REVERT: A 574 ARG cc_start: 0.7743 (tpp80) cc_final: 0.7271 (tpt170) REVERT: A 688 CYS cc_start: 0.8267 (p) cc_final: 0.8054 (p) REVERT: A 740 SER cc_start: 0.8711 (p) cc_final: 0.8504 (m) REVERT: A 802 ILE cc_start: 0.8936 (mt) cc_final: 0.8525 (tp) REVERT: A 848 GLU cc_start: 0.8207 (pt0) cc_final: 0.7967 (pt0) REVERT: A 926 ARG cc_start: 0.8881 (mtt180) cc_final: 0.8561 (mtt180) REVERT: A 947 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8006 (mp0) REVERT: A 949 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7750 (mt-10) REVERT: A 1013 ASP cc_start: 0.7725 (m-30) cc_final: 0.7342 (m-30) REVERT: A 1018 ARG cc_start: 0.7777 (mmt-90) cc_final: 0.7510 (mpt180) REVERT: A 1243 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6592 (mm-30) REVERT: A 1253 TRP cc_start: 0.8210 (t60) cc_final: 0.7982 (t-100) REVERT: A 1283 PHE cc_start: 0.7026 (m-80) cc_final: 0.6688 (m-10) REVERT: A 1395 ASP cc_start: 0.8127 (t70) cc_final: 0.7412 (t70) REVERT: B 126 GLU cc_start: 0.8636 (tt0) cc_final: 0.8377 (tt0) REVERT: B 127 MET cc_start: 0.8312 (tmm) cc_final: 0.8047 (ttp) REVERT: B 254 GLN cc_start: 0.8194 (tt0) cc_final: 0.7985 (tt0) REVERT: B 298 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7928 (mtpp) REVERT: D 128 LEU cc_start: 0.8031 (mm) cc_final: 0.7638 (mt) outliers start: 2 outliers final: 1 residues processed: 256 average time/residue: 1.4794 time to fit residues: 409.7061 Evaluate side-chains 199 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.9990 chunk 127 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 ASN A 624 ASN A 746 ASN A 764 GLN A1141 GLN A1156 GLN A1188 ASN A1270 ASN A1322 ASN A1374 ASN A1408 ASN C 161 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.147722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.109560 restraints weight = 13826.921| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.85 r_work: 0.2975 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13932 Z= 0.145 Angle : 0.599 10.684 18878 Z= 0.321 Chirality : 0.043 0.151 2107 Planarity : 0.005 0.042 2401 Dihedral : 4.912 26.041 1836 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.86 % Allowed : 7.32 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: 0.42 (0.20), residues: 1679 helix: 1.23 (0.18), residues: 871 sheet: 0.87 (0.50), residues: 86 loop : -0.97 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 76 HIS 0.006 0.001 HIS A 154 PHE 0.017 0.002 PHE A 372 TYR 0.019 0.002 TYR A 803 ARG 0.006 0.001 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.06587 ( 680) hydrogen bonds : angle 4.58456 ( 1926) metal coordination : bond 0.01467 ( 3) covalent geometry : bond 0.00300 (13929) covalent geometry : angle 0.59948 (18878) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 1.484 Fit side-chains REVERT: A 141 LYS cc_start: 0.8277 (ttpp) cc_final: 0.7849 (ttpt) REVERT: A 217 ARG cc_start: 0.6980 (mpp-170) cc_final: 0.6224 (mmt-90) REVERT: A 229 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7408 (tp30) REVERT: A 391 LYS cc_start: 0.8597 (tttt) cc_final: 0.8171 (ttpp) REVERT: A 431 LYS cc_start: 0.8293 (tptp) cc_final: 0.8013 (tptp) REVERT: A 536 GLU cc_start: 0.7852 (tp30) cc_final: 0.7448 (mm-30) REVERT: A 597 MET cc_start: 0.6078 (OUTLIER) cc_final: 0.5548 (ttm) REVERT: A 662 LYS cc_start: 0.6873 (ttpp) cc_final: 0.6582 (ttpp) REVERT: A 688 CYS cc_start: 0.8152 (p) cc_final: 0.7504 (m) REVERT: A 740 SER cc_start: 0.8835 (p) cc_final: 0.8632 (m) REVERT: A 762 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7295 (m-30) REVERT: A 778 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: A 802 ILE cc_start: 0.8613 (mt) cc_final: 0.8354 (tp) REVERT: A 820 LYS cc_start: 0.8992 (ttpt) cc_final: 0.8745 (ttmt) REVERT: A 926 ARG cc_start: 0.8952 (mtt180) cc_final: 0.8614 (mtt180) REVERT: A 947 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7973 (mp0) REVERT: A 992 ARG cc_start: 0.6982 (ttm-80) cc_final: 0.5861 (mtp180) REVERT: A 1000 GLN cc_start: 0.7933 (mt0) cc_final: 0.7698 (mt0) REVERT: A 1013 ASP cc_start: 0.7590 (m-30) cc_final: 0.7329 (m-30) REVERT: A 1018 ARG cc_start: 0.7766 (mmt-90) cc_final: 0.7451 (mpt180) REVERT: A 1073 MET cc_start: 0.7604 (mmm) cc_final: 0.7115 (tmm) REVERT: A 1104 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7069 (pt0) REVERT: A 1243 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6578 (mm-30) REVERT: A 1265 LEU cc_start: 0.8417 (mt) cc_final: 0.7933 (mm) REVERT: A 1283 PHE cc_start: 0.7058 (m-80) cc_final: 0.6723 (m-10) REVERT: A 1336 ASP cc_start: 0.6678 (t70) cc_final: 0.6237 (t0) REVERT: A 1360 LYS cc_start: 0.8461 (mttp) cc_final: 0.7938 (mptt) REVERT: B 254 GLN cc_start: 0.8373 (tt0) cc_final: 0.8136 (tt0) REVERT: B 268 ARG cc_start: 0.7662 (ttm170) cc_final: 0.7457 (ttm170) REVERT: C 166 LYS cc_start: 0.7596 (mptt) cc_final: 0.7242 (mmtt) REVERT: D 128 LEU cc_start: 0.8149 (mm) cc_final: 0.7724 (mt) REVERT: E 113 MET cc_start: 0.6236 (mmp) cc_final: 0.5653 (tpp) outliers start: 28 outliers final: 11 residues processed: 235 average time/residue: 1.4912 time to fit residues: 379.9301 Evaluate side-chains 215 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 200 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 597 MET Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain E residue 124 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 154 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN A 746 ASN A1188 ASN A1270 ASN A1322 ASN A1374 ASN A1408 ASN D 133 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.146035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.107315 restraints weight = 13982.702| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.85 r_work: 0.2943 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13932 Z= 0.158 Angle : 0.592 11.587 18878 Z= 0.312 Chirality : 0.043 0.159 2107 Planarity : 0.005 0.044 2401 Dihedral : 4.717 24.937 1834 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.20 % Allowed : 10.71 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: 0.56 (0.20), residues: 1679 helix: 1.34 (0.18), residues: 869 sheet: 1.20 (0.50), residues: 86 loop : -0.93 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.005 0.001 HIS A 687 PHE 0.026 0.002 PHE A 372 TYR 0.018 0.002 TYR A 803 ARG 0.005 0.000 ARG B 271 Details of bonding type rmsd hydrogen bonds : bond 0.06683 ( 680) hydrogen bonds : angle 4.35286 ( 1926) metal coordination : bond 0.01583 ( 3) covalent geometry : bond 0.00362 (13929) covalent geometry : angle 0.59231 (18878) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 1.500 Fit side-chains revert: symmetry clash REVERT: A 141 LYS cc_start: 0.8309 (ttpp) cc_final: 0.7919 (ttmm) REVERT: A 217 ARG cc_start: 0.7110 (mpp-170) cc_final: 0.6412 (mmt-90) REVERT: A 229 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7508 (tp30) REVERT: A 391 LYS cc_start: 0.8694 (tttt) cc_final: 0.8335 (ttpp) REVERT: A 436 LEU cc_start: 0.8102 (mm) cc_final: 0.7890 (mm) REVERT: A 443 ARG cc_start: 0.8165 (ttm-80) cc_final: 0.7945 (ttt180) REVERT: A 536 GLU cc_start: 0.8044 (tp30) cc_final: 0.7651 (mm-30) REVERT: A 572 ARG cc_start: 0.7701 (mtp85) cc_final: 0.7443 (mtp180) REVERT: A 597 MET cc_start: 0.6127 (OUTLIER) cc_final: 0.5882 (ttm) REVERT: A 657 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7892 (mtm180) REVERT: A 688 CYS cc_start: 0.8369 (p) cc_final: 0.7813 (m) REVERT: A 778 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.7926 (tm-30) REVERT: A 802 ILE cc_start: 0.8685 (mt) cc_final: 0.8475 (tp) REVERT: A 926 ARG cc_start: 0.9005 (mtt180) cc_final: 0.8726 (mtt180) REVERT: A 992 ARG cc_start: 0.7174 (ttm-80) cc_final: 0.6071 (mtp180) REVERT: A 1018 ARG cc_start: 0.7963 (mmt-90) cc_final: 0.7725 (mmt-90) REVERT: A 1073 MET cc_start: 0.7546 (mmm) cc_final: 0.7229 (tmm) REVERT: A 1104 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7280 (pt0) REVERT: A 1243 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6839 (mm-30) REVERT: A 1253 TRP cc_start: 0.8329 (t60) cc_final: 0.8097 (t-100) REVERT: A 1265 LEU cc_start: 0.8590 (mt) cc_final: 0.8082 (mm) REVERT: A 1283 PHE cc_start: 0.7247 (m-80) cc_final: 0.6870 (m-10) REVERT: A 1336 ASP cc_start: 0.6745 (t70) cc_final: 0.6199 (t0) REVERT: A 1360 LYS cc_start: 0.8548 (mttp) cc_final: 0.8306 (mttp) REVERT: B 254 GLN cc_start: 0.8583 (tt0) cc_final: 0.8347 (tt0) REVERT: C 166 LYS cc_start: 0.7755 (mptt) cc_final: 0.7373 (mmtt) REVERT: D 128 LEU cc_start: 0.8265 (mm) cc_final: 0.7903 (mt) outliers start: 33 outliers final: 15 residues processed: 218 average time/residue: 1.3631 time to fit residues: 322.6996 Evaluate side-chains 213 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 597 MET Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain E residue 124 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 92 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 157 optimal weight: 0.2980 chunk 149 optimal weight: 3.9990 chunk 37 optimal weight: 0.0060 chunk 23 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN A 746 ASN A1270 ASN A1322 ASN A1374 ASN A1408 ASN D 133 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.146760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.107939 restraints weight = 13897.036| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.87 r_work: 0.2941 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13932 Z= 0.149 Angle : 0.575 10.854 18878 Z= 0.302 Chirality : 0.043 0.165 2107 Planarity : 0.005 0.045 2401 Dihedral : 4.640 24.720 1834 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.53 % Allowed : 11.91 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: 0.73 (0.20), residues: 1679 helix: 1.47 (0.18), residues: 863 sheet: 1.33 (0.50), residues: 86 loop : -0.82 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.004 0.001 HIS A 154 PHE 0.023 0.002 PHE A 372 TYR 0.019 0.002 TYR A 803 ARG 0.006 0.000 ARG B 271 Details of bonding type rmsd hydrogen bonds : bond 0.06257 ( 680) hydrogen bonds : angle 4.24430 ( 1926) metal coordination : bond 0.01040 ( 3) covalent geometry : bond 0.00347 (13929) covalent geometry : angle 0.57519 (18878) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 1.486 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7395 (t0) REVERT: A 141 LYS cc_start: 0.8125 (ttpp) cc_final: 0.7668 (ttmm) REVERT: A 217 ARG cc_start: 0.7011 (mpp-170) cc_final: 0.6239 (mmt-90) REVERT: A 219 GLN cc_start: 0.7665 (mt0) cc_final: 0.7123 (mt0) REVERT: A 391 LYS cc_start: 0.8530 (tttt) cc_final: 0.8103 (ttpp) REVERT: A 443 ARG cc_start: 0.8002 (ttm-80) cc_final: 0.7728 (ttt180) REVERT: A 536 GLU cc_start: 0.7852 (tp30) cc_final: 0.7448 (mm-30) REVERT: A 572 ARG cc_start: 0.7561 (mtp85) cc_final: 0.7338 (mmm160) REVERT: A 657 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7646 (mtm180) REVERT: A 688 CYS cc_start: 0.8273 (p) cc_final: 0.7758 (m) REVERT: A 778 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: A 802 ILE cc_start: 0.8618 (mt) cc_final: 0.8295 (tp) REVERT: A 926 ARG cc_start: 0.8923 (mtt180) cc_final: 0.8652 (mtt180) REVERT: A 964 ASP cc_start: 0.7580 (m-30) cc_final: 0.7346 (p0) REVERT: A 992 ARG cc_start: 0.6875 (ttm-80) cc_final: 0.5754 (mtp180) REVERT: A 1018 ARG cc_start: 0.7770 (mmt-90) cc_final: 0.7483 (mmt-90) REVERT: A 1073 MET cc_start: 0.7362 (mmm) cc_final: 0.7000 (tmm) REVERT: A 1104 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7050 (pt0) REVERT: A 1253 TRP cc_start: 0.8326 (t60) cc_final: 0.8092 (t-100) REVERT: A 1283 PHE cc_start: 0.7214 (m-80) cc_final: 0.6815 (m-10) REVERT: A 1336 ASP cc_start: 0.6649 (t70) cc_final: 0.5961 (t0) REVERT: A 1360 LYS cc_start: 0.8473 (mttp) cc_final: 0.8220 (mttp) REVERT: B 254 GLN cc_start: 0.8377 (tt0) cc_final: 0.8141 (tt0) REVERT: B 268 ARG cc_start: 0.7668 (mtp180) cc_final: 0.7166 (ttm170) REVERT: C 166 LYS cc_start: 0.7540 (mptt) cc_final: 0.7199 (mmtm) REVERT: C 167 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.6872 (m-30) outliers start: 38 outliers final: 19 residues processed: 225 average time/residue: 1.4765 time to fit residues: 360.3278 Evaluate side-chains 224 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain E residue 124 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 118 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 81 optimal weight: 0.1980 chunk 119 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN A 746 ASN A1270 ASN A1322 ASN A1374 ASN A1408 ASN D 133 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.147609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.108949 restraints weight = 13928.891| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.85 r_work: 0.2977 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13932 Z= 0.130 Angle : 0.544 10.199 18878 Z= 0.285 Chirality : 0.041 0.162 2107 Planarity : 0.004 0.044 2401 Dihedral : 4.492 23.580 1834 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.79 % Allowed : 12.51 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: 0.97 (0.20), residues: 1679 helix: 1.65 (0.18), residues: 856 sheet: 1.41 (0.50), residues: 86 loop : -0.66 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.004 0.001 HIS A 154 PHE 0.023 0.002 PHE A 372 TYR 0.017 0.001 TYR A 803 ARG 0.004 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.05739 ( 680) hydrogen bonds : angle 4.15063 ( 1926) metal coordination : bond 0.00770 ( 3) covalent geometry : bond 0.00292 (13929) covalent geometry : angle 0.54356 (18878) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 1.610 Fit side-chains REVERT: A 9 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7457 (t0) REVERT: A 141 LYS cc_start: 0.8157 (ttpp) cc_final: 0.7752 (ttmm) REVERT: A 217 ARG cc_start: 0.7058 (mpp-170) cc_final: 0.6323 (mmt-90) REVERT: A 219 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7188 (mt0) REVERT: A 229 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7260 (tp30) REVERT: A 391 LYS cc_start: 0.8579 (tttt) cc_final: 0.8191 (ttpp) REVERT: A 443 ARG cc_start: 0.8108 (ttm-80) cc_final: 0.7851 (ttt180) REVERT: A 444 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7638 (pp30) REVERT: A 536 GLU cc_start: 0.7979 (tp30) cc_final: 0.7619 (mm-30) REVERT: A 657 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7711 (mtm180) REVERT: A 688 CYS cc_start: 0.8290 (p) cc_final: 0.7810 (m) REVERT: A 778 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7735 (tm-30) REVERT: A 802 ILE cc_start: 0.8607 (mt) cc_final: 0.8372 (tp) REVERT: A 992 ARG cc_start: 0.7054 (ttm-80) cc_final: 0.5939 (mtp180) REVERT: A 1018 ARG cc_start: 0.7850 (mmt-90) cc_final: 0.7563 (mmt-90) REVERT: A 1104 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7159 (pt0) REVERT: A 1253 TRP cc_start: 0.8357 (t60) cc_final: 0.8131 (t-100) REVERT: A 1283 PHE cc_start: 0.7330 (m-80) cc_final: 0.6920 (m-10) REVERT: A 1336 ASP cc_start: 0.6720 (t70) cc_final: 0.6053 (t0) REVERT: A 1360 LYS cc_start: 0.8494 (mttp) cc_final: 0.8254 (mttm) REVERT: B 140 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7209 (tmt170) REVERT: B 254 GLN cc_start: 0.8486 (tt0) cc_final: 0.8267 (tt0) REVERT: B 268 ARG cc_start: 0.7825 (mtp180) cc_final: 0.7307 (ttm170) REVERT: C 166 LYS cc_start: 0.7670 (mptt) cc_final: 0.7305 (mmtm) REVERT: C 167 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7022 (m-30) outliers start: 42 outliers final: 21 residues processed: 224 average time/residue: 1.3867 time to fit residues: 337.6454 Evaluate side-chains 226 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain E residue 124 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 123 optimal weight: 1.9990 chunk 58 optimal weight: 0.0670 chunk 12 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 ASN A1270 ASN A1322 ASN A1408 ASN D 133 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.146960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.108196 restraints weight = 13980.954| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.84 r_work: 0.2946 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13932 Z= 0.144 Angle : 0.562 10.414 18878 Z= 0.294 Chirality : 0.042 0.163 2107 Planarity : 0.004 0.047 2401 Dihedral : 4.509 24.145 1834 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.93 % Allowed : 13.17 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: 0.87 (0.20), residues: 1679 helix: 1.58 (0.18), residues: 863 sheet: 1.43 (0.50), residues: 86 loop : -0.75 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.004 0.001 HIS A 154 PHE 0.022 0.002 PHE A 372 TYR 0.017 0.002 TYR A 803 ARG 0.004 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.06060 ( 680) hydrogen bonds : angle 4.15349 ( 1926) metal coordination : bond 0.01043 ( 3) covalent geometry : bond 0.00332 (13929) covalent geometry : angle 0.56228 (18878) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 200 time to evaluate : 1.531 Fit side-chains REVERT: A 9 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7391 (t0) REVERT: A 141 LYS cc_start: 0.8097 (ttpp) cc_final: 0.7669 (ttmm) REVERT: A 217 ARG cc_start: 0.6966 (mpp-170) cc_final: 0.6192 (mmt-90) REVERT: A 219 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7087 (mt0) REVERT: A 229 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7232 (tp30) REVERT: A 391 LYS cc_start: 0.8472 (tttt) cc_final: 0.8054 (ttpp) REVERT: A 443 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7738 (ttt180) REVERT: A 536 GLU cc_start: 0.7871 (tp30) cc_final: 0.7497 (mm-30) REVERT: A 657 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7605 (mtm180) REVERT: A 688 CYS cc_start: 0.8178 (p) cc_final: 0.7717 (m) REVERT: A 778 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: A 802 ILE cc_start: 0.8589 (mt) cc_final: 0.8298 (tp) REVERT: A 884 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6846 (tt) REVERT: A 992 ARG cc_start: 0.6968 (ttm-80) cc_final: 0.5796 (mtp180) REVERT: A 1002 ARG cc_start: 0.7653 (ttp80) cc_final: 0.7372 (ttp-110) REVERT: A 1018 ARG cc_start: 0.7788 (mmt-90) cc_final: 0.7499 (mmt180) REVERT: A 1104 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7041 (pt0) REVERT: A 1253 TRP cc_start: 0.8313 (t60) cc_final: 0.8089 (t-100) REVERT: A 1283 PHE cc_start: 0.7312 (m-80) cc_final: 0.6892 (m-10) REVERT: A 1336 ASP cc_start: 0.6759 (OUTLIER) cc_final: 0.5935 (t0) REVERT: A 1360 LYS cc_start: 0.8458 (mttp) cc_final: 0.8188 (mttm) REVERT: B 254 GLN cc_start: 0.8381 (tt0) cc_final: 0.8156 (tt0) REVERT: B 268 ARG cc_start: 0.7715 (mtp180) cc_final: 0.7174 (ttm170) REVERT: C 166 LYS cc_start: 0.7555 (mptt) cc_final: 0.7192 (mmtm) REVERT: C 167 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.6920 (m-30) outliers start: 44 outliers final: 26 residues processed: 222 average time/residue: 1.4560 time to fit residues: 351.1366 Evaluate side-chains 233 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1336 ASP Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 133 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 ASN A 817 GLN A1270 ASN A1322 ASN A1408 ASN D 133 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.148722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.110448 restraints weight = 14009.728| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.81 r_work: 0.3001 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13932 Z= 0.113 Angle : 0.519 9.819 18878 Z= 0.271 Chirality : 0.040 0.159 2107 Planarity : 0.004 0.044 2401 Dihedral : 4.317 22.597 1834 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.53 % Allowed : 13.97 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: 1.12 (0.20), residues: 1679 helix: 1.77 (0.18), residues: 862 sheet: 1.49 (0.50), residues: 86 loop : -0.61 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 76 HIS 0.004 0.001 HIS A 154 PHE 0.021 0.001 PHE A 372 TYR 0.016 0.001 TYR A 803 ARG 0.005 0.000 ARG A 503 Details of bonding type rmsd hydrogen bonds : bond 0.05079 ( 680) hydrogen bonds : angle 4.05049 ( 1926) metal coordination : bond 0.00857 ( 3) covalent geometry : bond 0.00242 (13929) covalent geometry : angle 0.51855 (18878) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 1.511 Fit side-chains REVERT: A 9 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7444 (t0) REVERT: A 141 LYS cc_start: 0.8117 (ttpp) cc_final: 0.7753 (ttmm) REVERT: A 217 ARG cc_start: 0.6981 (mpp-170) cc_final: 0.6245 (mmt-90) REVERT: A 219 GLN cc_start: 0.7668 (mt0) cc_final: 0.7124 (mt0) REVERT: A 229 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7282 (tp30) REVERT: A 391 LYS cc_start: 0.8470 (tttt) cc_final: 0.7797 (pttp) REVERT: A 443 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7762 (ttt180) REVERT: A 444 GLN cc_start: 0.8161 (pp30) cc_final: 0.7915 (pt0) REVERT: A 536 GLU cc_start: 0.7871 (tp30) cc_final: 0.7499 (mm-30) REVERT: A 657 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7251 (mtm-85) REVERT: A 688 CYS cc_start: 0.8136 (p) cc_final: 0.7776 (m) REVERT: A 702 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.8133 (m110) REVERT: A 743 MET cc_start: 0.5262 (mtt) cc_final: 0.3294 (mpt) REVERT: A 778 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: A 802 ILE cc_start: 0.8532 (mt) cc_final: 0.8316 (tp) REVERT: A 884 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6782 (tt) REVERT: A 992 ARG cc_start: 0.7018 (ttm-80) cc_final: 0.5891 (mtp180) REVERT: A 1013 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6810 (m-30) REVERT: A 1018 ARG cc_start: 0.7868 (mmt-90) cc_final: 0.7603 (mmt180) REVERT: A 1104 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7169 (pt0) REVERT: A 1253 TRP cc_start: 0.8312 (t60) cc_final: 0.8104 (t-100) REVERT: A 1283 PHE cc_start: 0.7426 (m-80) cc_final: 0.6954 (m-10) REVERT: A 1336 ASP cc_start: 0.6738 (t70) cc_final: 0.5978 (t0) REVERT: A 1360 LYS cc_start: 0.8459 (mttp) cc_final: 0.8206 (mttm) REVERT: A 1395 ASP cc_start: 0.8172 (t70) cc_final: 0.7602 (t70) REVERT: B 254 GLN cc_start: 0.8437 (tt0) cc_final: 0.8218 (tt0) REVERT: C 166 LYS cc_start: 0.7651 (mptt) cc_final: 0.7304 (mmtm) REVERT: C 167 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.6973 (m-30) outliers start: 38 outliers final: 20 residues processed: 224 average time/residue: 1.3822 time to fit residues: 336.8034 Evaluate side-chains 229 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 133 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 20 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 127 optimal weight: 0.0070 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 ASN A1270 ASN A1322 ASN A1408 ASN D 133 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.148725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.110442 restraints weight = 14029.500| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.80 r_work: 0.2975 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13932 Z= 0.122 Angle : 0.531 10.089 18878 Z= 0.276 Chirality : 0.041 0.167 2107 Planarity : 0.004 0.044 2401 Dihedral : 4.302 22.921 1834 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.33 % Allowed : 14.30 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: 1.15 (0.20), residues: 1679 helix: 1.79 (0.18), residues: 862 sheet: 1.52 (0.50), residues: 86 loop : -0.59 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.004 0.001 HIS A 154 PHE 0.020 0.002 PHE A 372 TYR 0.015 0.001 TYR A 803 ARG 0.006 0.000 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.05365 ( 680) hydrogen bonds : angle 4.04368 ( 1926) metal coordination : bond 0.00779 ( 3) covalent geometry : bond 0.00272 (13929) covalent geometry : angle 0.53083 (18878) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 1.574 Fit side-chains REVERT: A 9 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7329 (t0) REVERT: A 141 LYS cc_start: 0.8087 (ttpp) cc_final: 0.7701 (ttmm) REVERT: A 217 ARG cc_start: 0.6913 (mpp-170) cc_final: 0.6108 (mmt-90) REVERT: A 219 GLN cc_start: 0.7662 (mt0) cc_final: 0.7151 (mt0) REVERT: A 229 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7279 (tp30) REVERT: A 391 LYS cc_start: 0.8457 (tttt) cc_final: 0.7753 (pttp) REVERT: A 536 GLU cc_start: 0.7839 (tp30) cc_final: 0.7463 (mm-30) REVERT: A 572 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7154 (mtm180) REVERT: A 657 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7241 (mtm-85) REVERT: A 688 CYS cc_start: 0.8223 (p) cc_final: 0.7902 (m) REVERT: A 702 ASN cc_start: 0.8462 (OUTLIER) cc_final: 0.8160 (m110) REVERT: A 743 MET cc_start: 0.5133 (mtt) cc_final: 0.3172 (mpt) REVERT: A 778 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: A 802 ILE cc_start: 0.8548 (mt) cc_final: 0.8291 (tp) REVERT: A 884 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6824 (tt) REVERT: A 992 ARG cc_start: 0.6989 (ttm-80) cc_final: 0.5825 (mtp180) REVERT: A 1018 ARG cc_start: 0.7806 (mmt-90) cc_final: 0.7537 (mmt-90) REVERT: A 1104 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7105 (pt0) REVERT: A 1243 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6940 (mt-10) REVERT: A 1253 TRP cc_start: 0.8273 (t60) cc_final: 0.8049 (t-100) REVERT: A 1283 PHE cc_start: 0.7360 (m-80) cc_final: 0.6892 (m-10) REVERT: A 1336 ASP cc_start: 0.6719 (OUTLIER) cc_final: 0.5901 (t0) REVERT: A 1360 LYS cc_start: 0.8426 (mttp) cc_final: 0.8162 (mttm) REVERT: A 1395 ASP cc_start: 0.8157 (t70) cc_final: 0.7584 (t70) REVERT: B 254 GLN cc_start: 0.8374 (tt0) cc_final: 0.8155 (tt0) REVERT: C 166 LYS cc_start: 0.7590 (mptt) cc_final: 0.7230 (mmtm) REVERT: C 167 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.6941 (m-30) outliers start: 35 outliers final: 23 residues processed: 216 average time/residue: 1.3899 time to fit residues: 326.8209 Evaluate side-chains 226 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1336 ASP Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain E residue 124 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 114 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 162 optimal weight: 0.2980 chunk 41 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 ASN A1270 ASN A1322 ASN A1408 ASN D 133 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.149153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.110790 restraints weight = 13896.964| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.80 r_work: 0.2973 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13932 Z= 0.118 Angle : 0.523 9.876 18878 Z= 0.272 Chirality : 0.041 0.165 2107 Planarity : 0.004 0.044 2401 Dihedral : 4.261 22.678 1834 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.40 % Allowed : 14.04 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: 1.18 (0.20), residues: 1679 helix: 1.82 (0.18), residues: 862 sheet: 1.52 (0.50), residues: 86 loop : -0.57 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.004 0.001 HIS A 154 PHE 0.020 0.001 PHE A 372 TYR 0.015 0.001 TYR A 803 ARG 0.005 0.000 ARG A 503 Details of bonding type rmsd hydrogen bonds : bond 0.05213 ( 680) hydrogen bonds : angle 4.02821 ( 1926) metal coordination : bond 0.00906 ( 3) covalent geometry : bond 0.00261 (13929) covalent geometry : angle 0.52286 (18878) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 1.508 Fit side-chains REVERT: A 9 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7329 (t0) REVERT: A 77 ASP cc_start: 0.7657 (t0) cc_final: 0.7129 (p0) REVERT: A 141 LYS cc_start: 0.8061 (ttpp) cc_final: 0.7653 (ttmm) REVERT: A 217 ARG cc_start: 0.6881 (mpp-170) cc_final: 0.6064 (mmt-90) REVERT: A 219 GLN cc_start: 0.7688 (mt0) cc_final: 0.7156 (mt0) REVERT: A 229 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7277 (tp30) REVERT: A 391 LYS cc_start: 0.8392 (tttt) cc_final: 0.7670 (pttp) REVERT: A 536 GLU cc_start: 0.7789 (tp30) cc_final: 0.7417 (mm-30) REVERT: A 572 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7105 (mtm180) REVERT: A 657 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7174 (mtm-85) REVERT: A 688 CYS cc_start: 0.8196 (p) cc_final: 0.7894 (m) REVERT: A 702 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.8157 (m110) REVERT: A 743 MET cc_start: 0.5091 (mtt) cc_final: 0.3169 (mpt) REVERT: A 778 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7626 (tm-30) REVERT: A 802 ILE cc_start: 0.8496 (mt) cc_final: 0.8236 (tp) REVERT: A 884 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6749 (tt) REVERT: A 992 ARG cc_start: 0.6967 (ttm-80) cc_final: 0.5788 (mtp180) REVERT: A 1018 ARG cc_start: 0.7764 (mmt-90) cc_final: 0.7489 (mmt-90) REVERT: A 1104 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7053 (pt0) REVERT: A 1243 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6899 (mt-10) REVERT: A 1253 TRP cc_start: 0.8273 (t60) cc_final: 0.8051 (t-100) REVERT: A 1283 PHE cc_start: 0.7374 (m-80) cc_final: 0.6906 (m-10) REVERT: A 1336 ASP cc_start: 0.6735 (OUTLIER) cc_final: 0.5923 (t0) REVERT: A 1360 LYS cc_start: 0.8390 (mttp) cc_final: 0.8115 (mttm) REVERT: A 1395 ASP cc_start: 0.8116 (t70) cc_final: 0.7573 (t70) REVERT: A 1402 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8210 (m-40) REVERT: B 254 GLN cc_start: 0.8323 (tt0) cc_final: 0.8098 (tt0) REVERT: C 166 LYS cc_start: 0.7541 (mptt) cc_final: 0.7177 (mmtm) REVERT: C 167 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.6906 (m-30) outliers start: 36 outliers final: 22 residues processed: 213 average time/residue: 1.3888 time to fit residues: 321.9887 Evaluate side-chains 223 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1336 ASP Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain A residue 1402 ASN Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain E residue 124 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 ASN A1270 ASN A1297 ASN A1408 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.146873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.108038 restraints weight = 13884.012| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.82 r_work: 0.2947 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13932 Z= 0.152 Angle : 0.570 10.531 18878 Z= 0.296 Chirality : 0.043 0.166 2107 Planarity : 0.004 0.046 2401 Dihedral : 4.432 24.384 1834 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.33 % Allowed : 14.24 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: 1.04 (0.20), residues: 1679 helix: 1.69 (0.18), residues: 862 sheet: 1.54 (0.50), residues: 86 loop : -0.63 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.005 0.001 HIS A 867 PHE 0.022 0.002 PHE A 372 TYR 0.017 0.002 TYR A 803 ARG 0.006 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.06207 ( 680) hydrogen bonds : angle 4.13487 ( 1926) metal coordination : bond 0.00933 ( 3) covalent geometry : bond 0.00357 (13929) covalent geometry : angle 0.56957 (18878) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 1.500 Fit side-chains REVERT: A 9 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.7389 (t0) REVERT: A 141 LYS cc_start: 0.8078 (ttpp) cc_final: 0.7693 (ttmm) REVERT: A 217 ARG cc_start: 0.6908 (mpp-170) cc_final: 0.6106 (mmt-90) REVERT: A 219 GLN cc_start: 0.7696 (mt0) cc_final: 0.7123 (mt0) REVERT: A 229 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7291 (tp30) REVERT: A 391 LYS cc_start: 0.8502 (tttt) cc_final: 0.8099 (ttpp) REVERT: A 536 GLU cc_start: 0.7956 (tp30) cc_final: 0.7595 (mm-30) REVERT: A 572 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7146 (mtm180) REVERT: A 657 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7613 (mtm180) REVERT: A 688 CYS cc_start: 0.8281 (p) cc_final: 0.7965 (m) REVERT: A 702 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8170 (m110) REVERT: A 743 MET cc_start: 0.5202 (mtt) cc_final: 0.3188 (mpt) REVERT: A 746 ASN cc_start: 0.7611 (m-40) cc_final: 0.7411 (m110) REVERT: A 778 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: A 802 ILE cc_start: 0.8622 (mt) cc_final: 0.8338 (tp) REVERT: A 884 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6830 (tt) REVERT: A 1018 ARG cc_start: 0.7853 (mmt-90) cc_final: 0.7563 (mmt-90) REVERT: A 1104 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7086 (pt0) REVERT: A 1143 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8043 (pt0) REVERT: A 1253 TRP cc_start: 0.8322 (t60) cc_final: 0.8099 (t-100) REVERT: A 1283 PHE cc_start: 0.7410 (m-80) cc_final: 0.6921 (m-10) REVERT: A 1336 ASP cc_start: 0.6812 (OUTLIER) cc_final: 0.5967 (t0) REVERT: A 1360 LYS cc_start: 0.8434 (mttp) cc_final: 0.8167 (mttm) REVERT: A 1395 ASP cc_start: 0.8124 (t70) cc_final: 0.7563 (t70) REVERT: B 254 GLN cc_start: 0.8411 (tt0) cc_final: 0.8193 (tt0) REVERT: C 167 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.6914 (m-30) outliers start: 35 outliers final: 22 residues processed: 216 average time/residue: 1.3649 time to fit residues: 320.6154 Evaluate side-chains 226 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1336 ASP Chi-restraints excluded: chain A residue 1367 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain E residue 124 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 122 optimal weight: 0.0270 chunk 23 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1270 ASN A1408 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.149317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.110911 restraints weight = 13952.169| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.80 r_work: 0.2990 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13932 Z= 0.109 Angle : 0.514 10.007 18878 Z= 0.267 Chirality : 0.040 0.163 2107 Planarity : 0.004 0.044 2401 Dihedral : 4.232 22.339 1834 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.26 % Allowed : 14.44 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: 1.20 (0.21), residues: 1679 helix: 1.83 (0.18), residues: 862 sheet: 1.58 (0.50), residues: 86 loop : -0.55 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 76 HIS 0.004 0.001 HIS A 154 PHE 0.019 0.001 PHE A 372 TYR 0.015 0.001 TYR A 803 ARG 0.008 0.000 ARG A1250 Details of bonding type rmsd hydrogen bonds : bond 0.04901 ( 680) hydrogen bonds : angle 4.03054 ( 1926) metal coordination : bond 0.00688 ( 3) covalent geometry : bond 0.00232 (13929) covalent geometry : angle 0.51352 (18878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11056.52 seconds wall clock time: 188 minutes 41.53 seconds (11321.53 seconds total)