Starting phenix.real_space_refine on Thu Sep 18 03:27:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ip2_60755/09_2025/9ip2_60755.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ip2_60755/09_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_60755/09_2025/9ip2_60755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ip2_60755/09_2025/9ip2_60755.map" model { file = "/net/cci-nas-00/data/ceres_data/9ip2_60755/09_2025/9ip2_60755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ip2_60755/09_2025/9ip2_60755.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.66, per 1000 atoms: 0.27 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: 1.13 Conformation dependent library (CDL) restraints added in 702.4 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.69 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: 2.52 Time building geometry restraints manager: 1.55 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: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.430 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.050 ------------------------------------------------------------------------------- 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 : 7.03 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.054 0.002 ARG A 26 TYR 0.086 0.005 TYR A 430 PHE 0.057 0.006 PHE A 529 TRP 0.065 0.006 TRP A1253 HIS 0.027 0.005 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.01229 (13929) covalent geometry : angle 1.44190 (18878) hydrogen bonds : bond 0.19347 ( 680) hydrogen bonds : angle 6.32314 ( 1926) metal coordination : bond 0.03387 ( 3) *********************** 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 : 0.565 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: 0.7322 time to fit residues: 201.7392 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 : 0.529 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.147503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.109212 restraints weight = 13947.143| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.87 r_work: 0.2970 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13932 Z= 0.142 Angle : 0.600 10.431 18878 Z= 0.322 Chirality : 0.043 0.150 2107 Planarity : 0.005 0.043 2401 Dihedral : 4.959 26.843 1836 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.86 % Allowed : 7.39 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.20), residues: 1679 helix: 1.21 (0.18), residues: 871 sheet: 0.95 (0.51), residues: 86 loop : -0.98 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 271 TYR 0.021 0.002 TYR A 803 PHE 0.018 0.002 PHE A 372 TRP 0.013 0.001 TRP A 76 HIS 0.005 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00297 (13929) covalent geometry : angle 0.60011 (18878) hydrogen bonds : bond 0.06505 ( 680) hydrogen bonds : angle 4.55586 ( 1926) metal coordination : bond 0.01575 ( 3) *********************** 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 252 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 224 time to evaluate : 0.540 Fit side-chains REVERT: A 141 LYS cc_start: 0.8267 (ttpp) cc_final: 0.7809 (ttpt) REVERT: A 196 LYS cc_start: 0.7644 (mptp) cc_final: 0.7332 (mmtm) REVERT: A 217 ARG cc_start: 0.6940 (mpp-170) cc_final: 0.6191 (mmt-90) REVERT: A 229 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7408 (tp30) REVERT: A 391 LYS cc_start: 0.8577 (tttt) cc_final: 0.8183 (ttpp) REVERT: A 431 LYS cc_start: 0.8291 (tptp) cc_final: 0.8010 (tptp) REVERT: A 536 GLU cc_start: 0.7878 (tp30) cc_final: 0.7447 (mm-30) REVERT: A 597 MET cc_start: 0.6074 (OUTLIER) cc_final: 0.5542 (ttm) REVERT: A 662 LYS cc_start: 0.6895 (ttpp) cc_final: 0.6535 (ttpp) REVERT: A 688 CYS cc_start: 0.8185 (p) cc_final: 0.7547 (m) REVERT: A 740 SER cc_start: 0.8838 (p) cc_final: 0.8626 (m) REVERT: A 762 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7296 (m-30) REVERT: A 778 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: A 802 ILE cc_start: 0.8611 (mt) cc_final: 0.8338 (tp) REVERT: A 820 LYS cc_start: 0.9009 (ttpt) cc_final: 0.8762 (ttmt) REVERT: A 848 GLU cc_start: 0.7877 (pt0) cc_final: 0.7633 (pt0) REVERT: A 926 ARG cc_start: 0.8963 (mtt180) cc_final: 0.8645 (mtt180) REVERT: A 947 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7978 (mp0) REVERT: A 992 ARG cc_start: 0.7061 (ttm-80) cc_final: 0.5903 (mtp180) REVERT: A 1000 GLN cc_start: 0.7940 (mt0) cc_final: 0.7705 (mt0) REVERT: A 1013 ASP cc_start: 0.7593 (m-30) cc_final: 0.7332 (m-30) REVERT: A 1018 ARG cc_start: 0.7763 (mmt-90) cc_final: 0.7541 (mpt180) REVERT: A 1073 MET cc_start: 0.7625 (mmm) cc_final: 0.7148 (tmm) REVERT: A 1104 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7106 (pt0) REVERT: A 1243 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6586 (mm-30) REVERT: A 1253 TRP cc_start: 0.8166 (t60) cc_final: 0.7966 (t-100) REVERT: A 1265 LEU cc_start: 0.8431 (mt) cc_final: 0.7991 (mm) REVERT: A 1283 PHE cc_start: 0.7098 (m-80) cc_final: 0.6755 (m-10) REVERT: A 1336 ASP cc_start: 0.6662 (t70) cc_final: 0.6235 (t0) REVERT: A 1360 LYS cc_start: 0.8461 (mttp) cc_final: 0.7935 (mptt) REVERT: B 254 GLN cc_start: 0.8380 (tt0) cc_final: 0.8131 (tt0) REVERT: C 166 LYS cc_start: 0.7516 (mptt) cc_final: 0.7124 (mmtt) REVERT: C 167 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6779 (m-30) REVERT: D 128 LEU cc_start: 0.8162 (mm) cc_final: 0.7726 (mt) REVERT: E 113 MET cc_start: 0.6269 (mmp) cc_final: 0.5688 (tpp) outliers start: 28 outliers final: 9 residues processed: 236 average time/residue: 0.7007 time to fit residues: 178.4986 Evaluate side-chains 215 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 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 B residue 142 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain C residue 167 ASP 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 30 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.142808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.104310 restraints weight = 14028.908| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.87 r_work: 0.2896 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13932 Z= 0.252 Angle : 0.705 13.129 18878 Z= 0.371 Chirality : 0.049 0.206 2107 Planarity : 0.006 0.050 2401 Dihedral : 5.131 27.567 1836 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.26 % Allowed : 11.04 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.20), residues: 1679 helix: 1.04 (0.18), residues: 863 sheet: 1.38 (0.52), residues: 86 loop : -1.12 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1046 TYR 0.021 0.002 TYR A 803 PHE 0.029 0.003 PHE A 372 TRP 0.013 0.003 TRP A 108 HIS 0.008 0.002 HIS A 707 Details of bonding type rmsd covalent geometry : bond 0.00628 (13929) covalent geometry : angle 0.70515 (18878) hydrogen bonds : bond 0.08555 ( 680) hydrogen bonds : angle 4.54129 ( 1926) metal coordination : bond 0.01629 ( 3) *********************** 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 234 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 141 LYS cc_start: 0.8300 (ttpp) cc_final: 0.7906 (ttmm) REVERT: A 217 ARG cc_start: 0.7189 (mpp-170) cc_final: 0.6337 (mmt-90) REVERT: A 229 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7298 (tp30) REVERT: A 391 LYS cc_start: 0.8714 (tttt) cc_final: 0.8300 (ttpp) REVERT: A 431 LYS cc_start: 0.8443 (tptp) cc_final: 0.8180 (tptt) REVERT: A 443 ARG cc_start: 0.8110 (ttm-80) cc_final: 0.7820 (ttt180) REVERT: A 536 GLU cc_start: 0.8041 (tp30) cc_final: 0.7684 (mm-30) REVERT: A 572 ARG cc_start: 0.7732 (mtp85) cc_final: 0.7475 (mtp180) REVERT: A 597 MET cc_start: 0.6140 (OUTLIER) cc_final: 0.5558 (ttm) REVERT: A 657 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7917 (mtm180) REVERT: A 740 SER cc_start: 0.8914 (p) cc_final: 0.8656 (m) REVERT: A 762 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7312 (m-30) REVERT: A 778 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.7796 (tm-30) REVERT: A 802 ILE cc_start: 0.8724 (mt) cc_final: 0.8423 (tp) REVERT: A 926 ARG cc_start: 0.8992 (mtt180) cc_final: 0.8733 (mtt180) REVERT: A 1002 ARG cc_start: 0.7794 (ttp80) cc_final: 0.7538 (ttp-110) REVERT: A 1018 ARG cc_start: 0.7891 (mmt-90) cc_final: 0.7594 (mmt-90) REVERT: A 1073 MET cc_start: 0.7693 (mmm) cc_final: 0.7244 (tmm) REVERT: A 1104 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7191 (pt0) REVERT: A 1253 TRP cc_start: 0.8431 (t60) cc_final: 0.8188 (t-100) REVERT: A 1283 PHE cc_start: 0.7288 (m-80) cc_final: 0.6906 (m-10) REVERT: A 1299 GLN cc_start: 0.6869 (tp-100) cc_final: 0.6390 (tp-100) REVERT: A 1336 ASP cc_start: 0.6827 (t70) cc_final: 0.6153 (t0) REVERT: A 1360 LYS cc_start: 0.8556 (mttp) cc_final: 0.8322 (mttp) REVERT: B 254 GLN cc_start: 0.8553 (tt0) cc_final: 0.8320 (tt0) REVERT: C 166 LYS cc_start: 0.7632 (mptt) cc_final: 0.7311 (mmtm) outliers start: 34 outliers final: 18 residues processed: 219 average time/residue: 0.7482 time to fit residues: 176.7743 Evaluate side-chains 220 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 248 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 584 LEU 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 762 ASP Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 997 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 C residue 135 VAL Chi-restraints excluded: chain C residue 152 LEU 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 55 optimal weight: 0.1980 chunk 98 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 chunk 159 optimal weight: 0.5980 chunk 53 optimal weight: 0.1980 chunk 103 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 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 = 0.3638 r_free = 0.3638 target = 0.149948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.111740 restraints weight = 14020.387| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.82 r_work: 0.3018 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13932 Z= 0.107 Angle : 0.520 10.663 18878 Z= 0.274 Chirality : 0.040 0.160 2107 Planarity : 0.004 0.044 2401 Dihedral : 4.520 23.670 1834 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.59 % Allowed : 11.58 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.20), residues: 1679 helix: 1.57 (0.18), residues: 856 sheet: 1.35 (0.50), residues: 86 loop : -0.70 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1040 TYR 0.017 0.001 TYR A 803 PHE 0.017 0.001 PHE A 372 TRP 0.012 0.001 TRP A 76 HIS 0.004 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00211 (13929) covalent geometry : angle 0.52041 (18878) hydrogen bonds : bond 0.04849 ( 680) hydrogen bonds : angle 4.17910 ( 1926) metal coordination : bond 0.01135 ( 3) *********************** 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 249 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7395 (t0) REVERT: A 141 LYS cc_start: 0.8132 (ttpp) cc_final: 0.7687 (ttmm) REVERT: A 196 LYS cc_start: 0.7641 (mptp) cc_final: 0.7327 (mmtm) REVERT: A 217 ARG cc_start: 0.6960 (mpp-170) cc_final: 0.6145 (mmt-90) REVERT: A 219 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7194 (mt0) REVERT: A 229 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7223 (tp30) REVERT: A 391 LYS cc_start: 0.8487 (tttt) cc_final: 0.8094 (ttpp) REVERT: A 443 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7769 (ttt180) REVERT: A 536 GLU cc_start: 0.7811 (tp30) cc_final: 0.7413 (mm-30) REVERT: A 657 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7608 (mtm180) REVERT: A 688 CYS cc_start: 0.8261 (p) cc_final: 0.7775 (m) REVERT: A 778 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: A 802 ILE cc_start: 0.8535 (mt) cc_final: 0.8289 (tp) REVERT: A 926 ARG cc_start: 0.8914 (mtt180) cc_final: 0.8599 (mtt180) REVERT: A 992 ARG cc_start: 0.6911 (ttm-80) cc_final: 0.5802 (mtp180) REVERT: A 1013 ASP cc_start: 0.7065 (OUTLIER) cc_final: 0.6775 (m-30) REVERT: A 1018 ARG cc_start: 0.7800 (mmt-90) cc_final: 0.7532 (mmt-90) REVERT: A 1101 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: A 1104 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7054 (pt0) REVERT: A 1253 TRP cc_start: 0.8249 (t60) cc_final: 0.8044 (t-100) REVERT: A 1283 PHE cc_start: 0.7255 (m-80) cc_final: 0.6867 (m-10) REVERT: A 1299 GLN cc_start: 0.6796 (tp-100) cc_final: 0.6351 (tp-100) REVERT: A 1336 ASP cc_start: 0.6653 (t70) cc_final: 0.6015 (t0) REVERT: A 1360 LYS cc_start: 0.8439 (mttp) cc_final: 0.8195 (mttp) REVERT: B 201 GLU cc_start: 0.7736 (mp0) cc_final: 0.7528 (mp0) REVERT: B 254 GLN cc_start: 0.8373 (tt0) cc_final: 0.8134 (tt0) REVERT: C 166 LYS cc_start: 0.7596 (mptt) cc_final: 0.7262 (mmtm) REVERT: C 167 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.6913 (m-30) outliers start: 39 outliers final: 16 residues processed: 228 average time/residue: 0.6740 time to fit residues: 166.4918 Evaluate side-chains 223 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 248 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 459 GLN 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 997 ILE Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1101 GLU 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 167 ASP Chi-restraints excluded: chain C residue 170 VAL 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 88 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 C 153 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 = 0.3556 r_free = 0.3556 target = 0.142787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.103713 restraints weight = 14026.348| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.85 r_work: 0.2888 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 13932 Z= 0.275 Angle : 0.709 13.567 18878 Z= 0.372 Chirality : 0.049 0.219 2107 Planarity : 0.006 0.061 2401 Dihedral : 4.996 26.880 1834 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.19 % Allowed : 12.71 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.20), residues: 1679 helix: 1.16 (0.18), residues: 852 sheet: 1.53 (0.51), residues: 86 loop : -1.06 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1046 TYR 0.020 0.003 TYR A 803 PHE 0.029 0.003 PHE A 372 TRP 0.014 0.003 TRP A 378 HIS 0.009 0.002 HIS A 707 Details of bonding type rmsd covalent geometry : bond 0.00693 (13929) covalent geometry : angle 0.70902 (18878) hydrogen bonds : bond 0.08529 ( 680) hydrogen bonds : angle 4.44450 ( 1926) metal coordination : bond 0.01540 ( 3) *********************** 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 252 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 204 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7422 (t0) REVERT: A 141 LYS cc_start: 0.8181 (ttpp) cc_final: 0.7783 (ttmm) REVERT: A 217 ARG cc_start: 0.7129 (mpp-170) cc_final: 0.6248 (mmt-90) REVERT: A 219 GLN cc_start: 0.7793 (mt0) cc_final: 0.7218 (mt0) REVERT: A 229 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7198 (tp30) REVERT: A 391 LYS cc_start: 0.8622 (tttt) cc_final: 0.8167 (ttpp) REVERT: A 443 ARG cc_start: 0.8030 (ttm-80) cc_final: 0.7806 (ttt180) REVERT: A 444 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7688 (pp30) REVERT: A 536 GLU cc_start: 0.8057 (tp30) cc_final: 0.7665 (mm-30) REVERT: A 572 ARG cc_start: 0.7696 (mtp85) cc_final: 0.7465 (mmm160) REVERT: A 688 CYS cc_start: 0.8286 (p) cc_final: 0.7684 (m) REVERT: A 702 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8146 (m110) REVERT: A 778 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: A 802 ILE cc_start: 0.8722 (mt) cc_final: 0.8430 (tp) REVERT: A 1002 ARG cc_start: 0.7677 (ttp80) cc_final: 0.7280 (ttp-110) REVERT: A 1018 ARG cc_start: 0.7849 (mmt-90) cc_final: 0.7584 (mmt-90) REVERT: A 1104 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7135 (pt0) REVERT: A 1253 TRP cc_start: 0.8403 (t60) cc_final: 0.8149 (t-100) REVERT: A 1283 PHE cc_start: 0.7359 (m-80) cc_final: 0.6934 (m-10) REVERT: A 1299 GLN cc_start: 0.6639 (tp-100) cc_final: 0.6233 (tp-100) REVERT: A 1336 ASP cc_start: 0.6789 (t70) cc_final: 0.5892 (t0) REVERT: A 1360 LYS cc_start: 0.8530 (mttp) cc_final: 0.8270 (mttm) REVERT: B 254 GLN cc_start: 0.8463 (tt0) cc_final: 0.8239 (tt0) REVERT: C 166 LYS cc_start: 0.7542 (mptt) cc_final: 0.7164 (mmtm) outliers start: 48 outliers final: 23 residues processed: 229 average time/residue: 0.6845 time to fit residues: 169.2117 Evaluate side-chains 224 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 149 MET 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 475 THR 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 702 ASN Chi-restraints excluded: chain A residue 778 GLU 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 1079 GLU Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1254 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 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 151 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.145857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.106893 restraints weight = 13929.992| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.82 r_work: 0.2929 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2405 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= 0.143 Angle : 0.572 11.041 18878 Z= 0.302 Chirality : 0.042 0.164 2107 Planarity : 0.005 0.047 2401 Dihedral : 4.712 25.569 1834 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.06 % Allowed : 13.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.20), residues: 1679 helix: 1.42 (0.18), residues: 852 sheet: 1.51 (0.51), residues: 86 loop : -0.94 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 503 TYR 0.019 0.001 TYR A 803 PHE 0.024 0.002 PHE A 372 TRP 0.009 0.001 TRP A 261 HIS 0.005 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00326 (13929) covalent geometry : angle 0.57249 (18878) hydrogen bonds : bond 0.06320 ( 680) hydrogen bonds : angle 4.26871 ( 1926) metal coordination : bond 0.01229 ( 3) *********************** 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 247 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 201 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7406 (t0) REVERT: A 141 LYS cc_start: 0.8130 (ttpp) cc_final: 0.7712 (ttmm) REVERT: A 217 ARG cc_start: 0.6915 (mpp-170) cc_final: 0.6048 (mmt-90) REVERT: A 219 GLN cc_start: 0.7704 (mt0) cc_final: 0.7170 (mt0) REVERT: A 229 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7190 (tp30) REVERT: A 391 LYS cc_start: 0.8484 (tttt) cc_final: 0.8065 (ttpp) REVERT: A 443 ARG cc_start: 0.8015 (ttm-80) cc_final: 0.7772 (ttt180) REVERT: A 536 GLU cc_start: 0.7968 (tp30) cc_final: 0.7589 (mm-30) REVERT: A 657 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7771 (mtt180) REVERT: A 688 CYS cc_start: 0.8271 (p) cc_final: 0.7718 (m) REVERT: A 702 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8160 (m110) REVERT: A 778 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7626 (tm-30) REVERT: A 802 ILE cc_start: 0.8570 (mt) cc_final: 0.8272 (tp) REVERT: A 884 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6879 (tt) REVERT: A 992 ARG cc_start: 0.6971 (ttm-80) cc_final: 0.5810 (mtp180) REVERT: A 1002 ARG cc_start: 0.7641 (ttp80) cc_final: 0.7342 (ttp-110) REVERT: A 1018 ARG cc_start: 0.7791 (mmt-90) cc_final: 0.7509 (mmt-90) REVERT: A 1104 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7084 (pt0) REVERT: A 1143 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8045 (pt0) REVERT: A 1253 TRP cc_start: 0.8400 (t60) cc_final: 0.8133 (t-100) REVERT: A 1283 PHE cc_start: 0.7379 (m-80) cc_final: 0.6920 (m-10) REVERT: A 1299 GLN cc_start: 0.6726 (tp-100) cc_final: 0.6243 (tp40) REVERT: A 1336 ASP cc_start: 0.6751 (OUTLIER) cc_final: 0.5886 (t0) REVERT: A 1360 LYS cc_start: 0.8466 (mttp) cc_final: 0.8201 (mttm) REVERT: B 140 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.6906 (tmt170) REVERT: B 254 GLN cc_start: 0.8389 (tt0) cc_final: 0.8161 (tt0) REVERT: C 166 LYS cc_start: 0.7503 (mptt) cc_final: 0.7108 (mmtm) REVERT: C 167 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.6866 (m-30) outliers start: 46 outliers final: 23 residues processed: 225 average time/residue: 0.6945 time to fit residues: 168.9216 Evaluate side-chains 228 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 149 MET 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 498 ASP Chi-restraints excluded: chain A residue 512 VAL 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 702 ASN Chi-restraints excluded: chain A residue 778 GLU 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 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 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 152 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 94 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 161 optimal weight: 0.3980 chunk 117 optimal weight: 6.9990 chunk 96 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.149242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.110929 restraints weight = 14006.486| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.78 r_work: 0.2997 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2610 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= 0.112 Angle : 0.518 9.712 18878 Z= 0.272 Chirality : 0.040 0.161 2107 Planarity : 0.004 0.045 2401 Dihedral : 4.369 22.270 1834 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.46 % Allowed : 13.91 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.20), residues: 1679 helix: 1.64 (0.18), residues: 862 sheet: 1.50 (0.50), residues: 86 loop : -0.64 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 503 TYR 0.015 0.001 TYR A 803 PHE 0.020 0.001 PHE A 372 TRP 0.010 0.001 TRP A 76 HIS 0.004 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00240 (13929) covalent geometry : angle 0.51834 (18878) hydrogen bonds : bond 0.04974 ( 680) hydrogen bonds : angle 4.09266 ( 1926) metal coordination : bond 0.00747 ( 3) *********************** 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 233 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 0.518 Fit side-chains REVERT: A 9 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7393 (t0) REVERT: A 77 ASP cc_start: 0.7571 (t0) cc_final: 0.7087 (p0) REVERT: A 141 LYS cc_start: 0.8024 (ttpp) cc_final: 0.7641 (ttmm) REVERT: A 196 LYS cc_start: 0.7690 (mptp) cc_final: 0.7326 (mmtm) REVERT: A 217 ARG cc_start: 0.6890 (mpp-170) cc_final: 0.6086 (mmt-90) REVERT: A 219 GLN cc_start: 0.7714 (mt0) cc_final: 0.7125 (mt0) REVERT: A 229 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7295 (tp30) REVERT: A 391 LYS cc_start: 0.8463 (tttt) cc_final: 0.8059 (ttpp) REVERT: A 536 GLU cc_start: 0.7878 (tp30) cc_final: 0.7513 (mm-30) REVERT: A 657 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7601 (mtm180) REVERT: A 688 CYS cc_start: 0.8205 (p) cc_final: 0.7734 (m) REVERT: A 743 MET cc_start: 0.5257 (mtt) cc_final: 0.3227 (mpt) REVERT: A 746 ASN cc_start: 0.7463 (m-40) cc_final: 0.7247 (m110) REVERT: A 778 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: A 802 ILE cc_start: 0.8544 (mt) cc_final: 0.8281 (tp) REVERT: A 884 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6786 (tt) REVERT: A 992 ARG cc_start: 0.6906 (ttm-80) cc_final: 0.5783 (mtp180) REVERT: A 1018 ARG cc_start: 0.7823 (mmt-90) cc_final: 0.7559 (mmt-90) REVERT: A 1104 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7068 (pt0) REVERT: A 1253 TRP cc_start: 0.8289 (t60) cc_final: 0.8042 (t-100) REVERT: A 1283 PHE cc_start: 0.7414 (m-80) cc_final: 0.6928 (m-10) REVERT: A 1299 GLN cc_start: 0.6875 (tp-100) cc_final: 0.6481 (tp-100) REVERT: A 1336 ASP cc_start: 0.6732 (OUTLIER) cc_final: 0.5915 (t0) REVERT: A 1360 LYS cc_start: 0.8411 (mttp) cc_final: 0.8166 (mttm) REVERT: A 1395 ASP cc_start: 0.8188 (t0) cc_final: 0.7575 (t70) REVERT: B 254 GLN cc_start: 0.8354 (tt0) cc_final: 0.8131 (tt0) REVERT: C 166 LYS cc_start: 0.7573 (mptt) cc_final: 0.7195 (mmtm) REVERT: C 167 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.6939 (m-30) outliers start: 37 outliers final: 19 residues processed: 212 average time/residue: 0.6494 time to fit residues: 149.4953 Evaluate side-chains 219 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 512 VAL 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 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 1251 LEU Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1336 ASP 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 152 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 78 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 118 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 GLN A1270 ASN A1322 ASN A1402 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 = 0.147416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.108962 restraints weight = 13936.318| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.85 r_work: 0.2960 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2573 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= 0.137 Angle : 0.550 10.042 18878 Z= 0.288 Chirality : 0.042 0.167 2107 Planarity : 0.004 0.045 2401 Dihedral : 4.430 23.441 1834 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.53 % Allowed : 14.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.20), residues: 1679 helix: 1.64 (0.18), residues: 862 sheet: 1.56 (0.51), residues: 86 loop : -0.66 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 53 TYR 0.016 0.001 TYR A 803 PHE 0.022 0.002 PHE A 372 TRP 0.009 0.001 TRP A 261 HIS 0.004 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00313 (13929) covalent geometry : angle 0.55045 (18878) hydrogen bonds : bond 0.05802 ( 680) hydrogen bonds : angle 4.12987 ( 1926) metal coordination : bond 0.00817 ( 3) *********************** 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 240 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 0.500 Fit side-chains REVERT: A 9 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7363 (t0) REVERT: A 77 ASP cc_start: 0.7647 (t0) cc_final: 0.7146 (p0) REVERT: A 141 LYS cc_start: 0.8043 (ttpp) cc_final: 0.7663 (ttmm) REVERT: A 217 ARG cc_start: 0.6898 (mpp-170) cc_final: 0.6087 (mmt-90) REVERT: A 219 GLN cc_start: 0.7676 (mt0) cc_final: 0.7093 (mt0) REVERT: A 229 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7261 (tp30) REVERT: A 391 LYS cc_start: 0.8500 (tttt) cc_final: 0.8076 (ttpp) REVERT: A 536 GLU cc_start: 0.7914 (tp30) cc_final: 0.7546 (mm-30) REVERT: A 657 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7636 (mtm180) REVERT: A 688 CYS cc_start: 0.8210 (p) cc_final: 0.7763 (m) REVERT: A 702 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.8175 (m110) REVERT: A 743 MET cc_start: 0.5191 (mtt) cc_final: 0.3183 (mpt) REVERT: A 746 ASN cc_start: 0.7495 (m-40) cc_final: 0.7290 (m110) REVERT: A 778 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: A 802 ILE cc_start: 0.8591 (mt) cc_final: 0.8292 (tp) REVERT: A 884 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6831 (tt) REVERT: A 992 ARG cc_start: 0.7002 (ttm-80) cc_final: 0.5843 (mtp180) REVERT: A 1018 ARG cc_start: 0.7832 (mmt-90) cc_final: 0.7550 (mmt-90) REVERT: A 1073 MET cc_start: 0.7480 (ttm) cc_final: 0.7081 (ttt) REVERT: A 1104 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7055 (pt0) REVERT: A 1253 TRP cc_start: 0.8336 (t60) cc_final: 0.8104 (t-100) REVERT: A 1283 PHE cc_start: 0.7441 (m-80) cc_final: 0.6965 (m-10) REVERT: A 1299 GLN cc_start: 0.6854 (tp-100) cc_final: 0.6466 (tp-100) REVERT: A 1336 ASP cc_start: 0.6791 (OUTLIER) cc_final: 0.5936 (t0) REVERT: A 1360 LYS cc_start: 0.8401 (mttp) cc_final: 0.8166 (mttm) REVERT: B 254 GLN cc_start: 0.8387 (tt0) cc_final: 0.8167 (tt0) REVERT: C 166 LYS cc_start: 0.7544 (mptt) cc_final: 0.7147 (mmtm) REVERT: C 167 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.6950 (m-30) outliers start: 38 outliers final: 21 residues processed: 221 average time/residue: 0.6278 time to fit residues: 151.0693 Evaluate side-chains 225 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 512 VAL 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 778 GLU 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 1251 LEU Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1336 ASP 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 152 LEU Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain E residue 113 MET 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 57 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 60 optimal weight: 0.0870 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- 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 817 GLN A1270 ASN A1322 ASN A1402 ASN A1408 ASN 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 = 0.149100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.110688 restraints weight = 14044.473| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.83 r_work: 0.2995 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13932 Z= 0.115 Angle : 0.521 9.676 18878 Z= 0.272 Chirality : 0.041 0.165 2107 Planarity : 0.004 0.044 2401 Dihedral : 4.302 22.396 1834 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.13 % Allowed : 14.90 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.20), residues: 1679 helix: 1.74 (0.18), residues: 862 sheet: 1.57 (0.51), residues: 86 loop : -0.61 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 503 TYR 0.015 0.001 TYR A 803 PHE 0.020 0.001 PHE A 372 TRP 0.008 0.001 TRP A 76 HIS 0.005 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00250 (13929) covalent geometry : angle 0.52059 (18878) hydrogen bonds : bond 0.05108 ( 680) hydrogen bonds : angle 4.07108 ( 1926) metal coordination : bond 0.00977 ( 3) *********************** 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 228 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.434 Fit side-chains REVERT: A 9 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7355 (t0) REVERT: A 77 ASP cc_start: 0.7609 (t0) cc_final: 0.7125 (p0) REVERT: A 141 LYS cc_start: 0.8048 (ttpp) cc_final: 0.7654 (ttmm) REVERT: A 217 ARG cc_start: 0.6861 (mpp-170) cc_final: 0.6059 (mmt-90) REVERT: A 219 GLN cc_start: 0.7680 (mt0) cc_final: 0.7098 (mt0) REVERT: A 391 LYS cc_start: 0.8444 (tttt) cc_final: 0.8029 (ttpp) REVERT: A 536 GLU cc_start: 0.7875 (tp30) cc_final: 0.7501 (mm-30) REVERT: A 572 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7123 (mtm180) REVERT: A 657 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7177 (mtm-85) REVERT: A 662 LYS cc_start: 0.6539 (ttpp) cc_final: 0.6246 (pttm) REVERT: A 688 CYS cc_start: 0.8128 (p) cc_final: 0.7726 (m) REVERT: A 743 MET cc_start: 0.5129 (mtt) cc_final: 0.3182 (mpt) REVERT: A 778 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: A 802 ILE cc_start: 0.8520 (mt) cc_final: 0.8249 (tp) REVERT: A 884 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6743 (tt) REVERT: A 992 ARG cc_start: 0.6891 (ttm-80) cc_final: 0.5756 (mtp180) REVERT: A 1018 ARG cc_start: 0.7815 (mmt-90) cc_final: 0.7541 (mmt-90) REVERT: A 1073 MET cc_start: 0.7386 (ttm) cc_final: 0.6987 (ttt) REVERT: A 1104 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7030 (pt0) REVERT: A 1143 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8047 (pt0) REVERT: A 1253 TRP cc_start: 0.8320 (t60) cc_final: 0.8085 (t-100) REVERT: A 1283 PHE cc_start: 0.7438 (m-80) cc_final: 0.6957 (m-10) REVERT: A 1299 GLN cc_start: 0.6801 (tp-100) cc_final: 0.6419 (tp-100) REVERT: A 1336 ASP cc_start: 0.6809 (OUTLIER) cc_final: 0.5973 (t0) REVERT: A 1360 LYS cc_start: 0.8385 (mttp) cc_final: 0.8143 (mttm) REVERT: A 1395 ASP cc_start: 0.8214 (t70) cc_final: 0.7759 (t0) REVERT: B 254 GLN cc_start: 0.8337 (tt0) cc_final: 0.8115 (tt0) REVERT: C 166 LYS cc_start: 0.7515 (mptt) cc_final: 0.7127 (mmtm) REVERT: C 167 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.6886 (m-30) outliers start: 32 outliers final: 21 residues processed: 211 average time/residue: 0.6601 time to fit residues: 150.5789 Evaluate side-chains 221 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 498 ASP 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 778 GLU 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 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 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 152 LEU Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain E residue 113 MET 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 157 optimal weight: 0.0770 chunk 162 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 66 optimal weight: 0.4980 chunk 61 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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** A 746 ASN A 817 GLN A1270 ASN A1297 ASN A1322 ASN A1408 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.150432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.112159 restraints weight = 14023.461| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.79 r_work: 0.3005 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13932 Z= 0.105 Angle : 0.506 9.678 18878 Z= 0.263 Chirality : 0.040 0.165 2107 Planarity : 0.004 0.043 2401 Dihedral : 4.190 21.598 1834 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.00 % Allowed : 15.04 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.21), residues: 1679 helix: 1.82 (0.18), residues: 862 sheet: 1.57 (0.51), residues: 86 loop : -0.53 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 53 TYR 0.015 0.001 TYR A 237 PHE 0.018 0.001 PHE A 372 TRP 0.009 0.001 TRP A 76 HIS 0.004 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00222 (13929) covalent geometry : angle 0.50646 (18878) hydrogen bonds : bond 0.04690 ( 680) hydrogen bonds : angle 4.03079 ( 1926) metal coordination : bond 0.00650 ( 3) ********************** 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 226 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7344 (t0) REVERT: A 77 ASP cc_start: 0.7571 (t0) cc_final: 0.7101 (p0) REVERT: A 141 LYS cc_start: 0.8048 (ttpp) cc_final: 0.7636 (ttmm) REVERT: A 217 ARG cc_start: 0.6836 (mpp-170) cc_final: 0.6034 (mmt-90) REVERT: A 219 GLN cc_start: 0.7665 (mt0) cc_final: 0.7135 (mt0) REVERT: A 274 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7469 (p0) REVERT: A 391 LYS cc_start: 0.8372 (tttt) cc_final: 0.7687 (pttp) REVERT: A 443 ARG cc_start: 0.7983 (ttm-80) cc_final: 0.7694 (ttt180) REVERT: A 536 GLU cc_start: 0.7870 (tp30) cc_final: 0.7642 (mm-30) REVERT: A 572 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7142 (mtm180) REVERT: A 662 LYS cc_start: 0.6562 (ttpp) cc_final: 0.6336 (pttm) REVERT: A 688 CYS cc_start: 0.8125 (p) cc_final: 0.7737 (m) REVERT: A 743 MET cc_start: 0.5062 (mtt) cc_final: 0.3168 (mpt) REVERT: A 778 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7628 (tm-30) REVERT: A 802 ILE cc_start: 0.8486 (mt) cc_final: 0.8227 (tp) REVERT: A 992 ARG cc_start: 0.6841 (ttm-80) cc_final: 0.5712 (mtp180) REVERT: A 1018 ARG cc_start: 0.7777 (mmt-90) cc_final: 0.7505 (mmt-90) REVERT: A 1073 MET cc_start: 0.7285 (ttm) cc_final: 0.6889 (ttt) REVERT: A 1104 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7009 (pt0) REVERT: A 1253 TRP cc_start: 0.8278 (t60) cc_final: 0.8032 (t-100) REVERT: A 1283 PHE cc_start: 0.7356 (m-80) cc_final: 0.6878 (m-10) REVERT: A 1299 GLN cc_start: 0.6752 (tp-100) cc_final: 0.6368 (tp-100) REVERT: A 1336 ASP cc_start: 0.6731 (OUTLIER) cc_final: 0.5890 (t0) REVERT: A 1360 LYS cc_start: 0.8356 (mttp) cc_final: 0.8105 (mttm) REVERT: A 1395 ASP cc_start: 0.8172 (t70) cc_final: 0.7779 (t0) REVERT: B 254 GLN cc_start: 0.8323 (tt0) cc_final: 0.8100 (tt0) REVERT: C 166 LYS cc_start: 0.7557 (mptt) cc_final: 0.7180 (mmtm) REVERT: C 167 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.6859 (m-30) outliers start: 30 outliers final: 21 residues processed: 211 average time/residue: 0.7073 time to fit residues: 161.5905 Evaluate side-chains 222 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 498 ASP 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 778 GLU 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 1254 VAL Chi-restraints excluded: chain A residue 1336 ASP 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 152 LEU Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain E residue 113 MET 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 38 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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** A 746 ASN A 817 GLN A1270 ASN A1408 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.144958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.105985 restraints weight = 13969.833| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.80 r_work: 0.2922 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13932 Z= 0.207 Angle : 0.632 11.758 18878 Z= 0.329 Chirality : 0.046 0.175 2107 Planarity : 0.005 0.048 2401 Dihedral : 4.639 25.529 1834 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.06 % Allowed : 15.04 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.20), residues: 1679 helix: 1.43 (0.18), residues: 863 sheet: 1.63 (0.51), residues: 86 loop : -0.77 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 53 TYR 0.020 0.002 TYR A 803 PHE 0.025 0.002 PHE A 372 TRP 0.012 0.002 TRP A 378 HIS 0.006 0.001 HIS A 707 Details of bonding type rmsd covalent geometry : bond 0.00510 (13929) covalent geometry : angle 0.63200 (18878) hydrogen bonds : bond 0.07284 ( 680) hydrogen bonds : angle 4.26705 ( 1926) metal coordination : bond 0.01451 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5406.73 seconds wall clock time: 92 minutes 46.09 seconds (5566.09 seconds total)