Starting phenix.real_space_refine on Thu Jun 12 05:20:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ip4_60757/06_2025/9ip4_60757.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ip4_60757/06_2025/9ip4_60757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ip4_60757/06_2025/9ip4_60757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ip4_60757/06_2025/9ip4_60757.map" model { file = "/net/cci-nas-00/data/ceres_data/9ip4_60757/06_2025/9ip4_60757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ip4_60757/06_2025/9ip4_60757.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.044 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 8743 2.51 5 N 2313 2.21 5 O 2489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13615 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1364, 11049 Classifications: {'peptide': 1364} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1304} Chain breaks: 5 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 8887 SG CYS A1108 65.500 72.380 21.911 1.00119.43 S ATOM 10719 SG CYS A1376 68.913 70.519 22.769 1.00126.27 S ATOM 10725 SG CYS A1377 66.627 71.766 25.182 1.00 86.82 S Time building chain proxies: 8.68, per 1000 atoms: 0.64 Number of scatterers: 13615 At special positions: 0 Unit cell: (98.716, 128.501, 127.65, 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 2489 8.00 N 2313 7.00 C 8743 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A1377 " pdb="ZN ZN A2001 " - pdb=" SG CYS A1376 " pdb="ZN ZN A2001 " - pdb=" SG CYS A1108 " 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3242 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 9 sheets defined 60.7% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 18 through 28 removed outlier: 4.173A pdb=" N ASP A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 removed outlier: 4.369A 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: 4.133A pdb=" N ASP A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N HIS A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 95 removed outlier: 4.110A pdb=" N VAL A 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ASP A 92 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 3.606A 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 removed outlier: 3.514A pdb=" N GLN A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) 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: 3.538A 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: 3.847A 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: 4.520A pdb=" N GLN A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.629A 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: 4.037A pdb=" N LYS A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 427 Processing helix chain 'A' and resid 435 through 438 removed outlier: 3.517A 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: 3.741A pdb=" N GLN A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS A 445 " --> pdb=" O TYR A 441 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 466 removed outlier: 3.608A pdb=" N PHE A 466 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 501 removed outlier: 3.883A pdb=" N TRP A 497 " --> pdb=" O GLN A 494 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER A 499 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 4.161A 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: 3.688A pdb=" N LEU A 524 " --> pdb=" O PRO A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 540 removed outlier: 3.837A 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: 3.913A 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 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: 3.847A pdb=" N ASN A 640 " --> pdb=" O GLU A 637 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU A 641 " --> pdb=" O LYS A 638 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE A 643 " --> pdb=" O ASN A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 660 removed outlier: 5.780A pdb=" N HIS A 650 " --> pdb=" O GLU A 646 " (cutoff:3.500A) removed outlier: 4.994A 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: 4.393A pdb=" N ASN A 695 " --> pdb=" O ASP A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 735 Processing helix chain 'A' and resid 760 through 785 removed outlier: 3.633A pdb=" N GLU A 769 " --> pdb=" O GLU A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 795 Processing helix chain 'A' and resid 817 through 823 removed outlier: 4.378A pdb=" N THR A 821 " --> pdb=" O GLN A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 853 Processing helix chain 'A' and resid 857 through 878 removed outlier: 3.703A 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: 3.716A 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: 3.629A pdb=" N SER A 957 " --> pdb=" O TYR A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 971 removed outlier: 3.710A pdb=" N PHE A 968 " --> pdb=" O ASP A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 981 removed outlier: 3.594A pdb=" N SER A 980 " --> pdb=" O VAL A 977 " (cutoff:3.500A) removed outlier: 3.565A 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: 3.808A pdb=" N LEU A 987 " --> pdb=" O ILE A 983 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLN A 989 " --> pdb=" O THR A 985 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N THR A 990 " --> pdb=" O PHE A 986 " (cutoff:3.500A) removed outlier: 3.625A 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: 3.528A pdb=" N GLU A1015 " --> pdb=" O GLY A1011 " (cutoff:3.500A) removed outlier: 3.750A 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: 4.543A 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 removed outlier: 3.559A pdb=" N TRP A1121 " --> pdb=" O ARG A1117 " (cutoff:3.500A) 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: 3.767A pdb=" N GLU A1155 " --> pdb=" O GLU A1151 " (cutoff:3.500A) removed outlier: 3.910A 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: 4.393A pdb=" N GLY A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) removed outlier: 4.207A 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: 4.119A 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 1281 removed outlier: 3.878A pdb=" N VAL A1280 " --> pdb=" O ASP A1276 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A1281 " --> pdb=" O TYR A1277 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1276 through 1281' Processing helix chain 'A' and resid 1282 through 1284 No H-bonds generated for 'chain 'A' and resid 1282 through 1284' Processing helix chain 'A' and resid 1291 through 1301 removed outlier: 4.233A pdb=" N ASN A1297 " --> pdb=" O VAL A1293 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP A1298 " --> pdb=" O HIS A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1315 Processing helix chain 'A' and resid 1324 through 1328 Processing helix chain 'A' and resid 1340 through 1356 removed outlier: 3.759A pdb=" N THR A1344 " --> pdb=" O ILE A1340 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE A1345 " --> pdb=" O PHE A1341 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN A1346 " --> pdb=" O GLN A1342 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A1356 " --> pdb=" O LEU A1352 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 138 removed outlier: 4.088A 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: 3.815A 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: 4.494A 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: 3.568A 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: 4.590A pdb=" N GLU D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 135 removed outlier: 3.608A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 69 removed outlier: 5.820A pdb=" N VAL A 232 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU A 68 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 8.207A 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 removed outlier: 4.588A pdb=" N PHE A 551 " --> pdb=" O TYR A 676 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS A 678 " --> pdb=" O PHE A 551 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 737 through 742 removed outlier: 4.257A 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: 6.077A 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: 6.852A pdb=" N THR A1368 " --> pdb=" O ILE A1147 " (cutoff:3.500A) removed outlier: 5.303A 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: 3.808A 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: 3.982A pdb=" N CYS B 315 " --> pdb=" O LEU B 327 " (cutoff:3.500A) 684 hydrogen bonds defined for protein. 1932 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: 5.26 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4248 1.34 - 1.47: 3485 1.47 - 1.60: 6099 1.60 - 1.73: 4 1.73 - 1.87: 103 Bond restraints: 13939 Sorted by residual: bond pdb=" CA PRO C 158 " pdb=" C PRO C 158 " ideal model delta sigma weight residual 1.517 1.603 -0.086 6.70e-03 2.23e+04 1.63e+02 bond pdb=" CA PRO C 159 " pdb=" C PRO C 159 " ideal model delta sigma weight residual 1.514 1.547 -0.033 5.50e-03 3.31e+04 3.56e+01 bond pdb=" CA PRO B 281 " pdb=" C PRO B 281 " ideal model delta sigma weight residual 1.514 1.547 -0.033 5.50e-03 3.31e+04 3.54e+01 bond pdb=" C PRO C 158 " pdb=" O PRO C 158 " ideal model delta sigma weight residual 1.243 1.207 0.036 8.50e-03 1.38e+04 1.79e+01 bond pdb=" SD MET C 124 " pdb=" CE MET C 124 " ideal model delta sigma weight residual 1.791 1.690 0.101 2.50e-02 1.60e+03 1.64e+01 ... (remaining 13934 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.82: 18767 4.82 - 9.63: 104 9.63 - 14.45: 13 14.45 - 19.26: 8 19.26 - 24.08: 1 Bond angle restraints: 18893 Sorted by residual: angle pdb=" O PRO C 158 " pdb=" C PRO C 158 " pdb=" N PRO C 159 " ideal model delta sigma weight residual 121.15 127.68 -6.53 4.70e-01 4.53e+00 1.93e+02 angle pdb=" N CYS A 892 " pdb=" CA CYS A 892 " pdb=" C CYS A 892 " ideal model delta sigma weight residual 111.14 119.97 -8.83 1.08e+00 8.57e-01 6.68e+01 angle pdb=" N GLN A 515 " pdb=" CA GLN A 515 " pdb=" C GLN A 515 " ideal model delta sigma weight residual 111.14 119.75 -8.61 1.08e+00 8.57e-01 6.36e+01 angle pdb=" CG MET A 743 " pdb=" SD MET A 743 " pdb=" CE MET A 743 " ideal model delta sigma weight residual 100.90 117.97 -17.07 2.20e+00 2.07e-01 6.02e+01 angle pdb=" CA GLU A 794 " pdb=" CB GLU A 794 " pdb=" CG GLU A 794 " ideal model delta sigma weight residual 114.10 129.17 -15.07 2.00e+00 2.50e-01 5.68e+01 ... (remaining 18888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7670 17.93 - 35.85: 587 35.85 - 53.78: 87 53.78 - 71.70: 14 71.70 - 89.63: 11 Dihedral angle restraints: 8369 sinusoidal: 3368 harmonic: 5001 Sorted by residual: dihedral pdb=" CA ILE A 711 " pdb=" C ILE A 711 " pdb=" N GLU A 712 " pdb=" CA GLU A 712 " ideal model delta harmonic sigma weight residual -180.00 -154.57 -25.43 0 5.00e+00 4.00e-02 2.59e+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 -156.31 -23.69 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA GLY A 805 " pdb=" C GLY A 805 " pdb=" N LYS A 806 " pdb=" CA LYS A 806 " ideal model delta harmonic sigma weight residual 180.00 157.38 22.62 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 8366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2006 0.113 - 0.227: 87 0.227 - 0.340: 11 0.340 - 0.454: 2 0.454 - 0.567: 2 Chirality restraints: 2108 Sorted by residual: chirality pdb=" CG LEU A1099 " pdb=" CB LEU A1099 " pdb=" CD1 LEU A1099 " pdb=" CD2 LEU A1099 " both_signs ideal model delta sigma weight residual False -2.59 -2.02 -0.57 2.00e-01 2.50e+01 8.04e+00 chirality pdb=" CG LEU A 828 " pdb=" CB LEU A 828 " pdb=" CD1 LEU A 828 " pdb=" CD2 LEU A 828 " both_signs ideal model delta sigma weight residual False -2.59 -3.06 0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" CA LYS A 517 " pdb=" N LYS A 517 " pdb=" C LYS A 517 " pdb=" CB LYS A 517 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 2105 not shown) Planarity restraints: 2404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1106 " -0.019 2.00e-02 2.50e+03 4.94e-02 4.27e+01 pdb=" CG PHE A1106 " 0.098 2.00e-02 2.50e+03 pdb=" CD1 PHE A1106 " -0.072 2.00e-02 2.50e+03 pdb=" CD2 PHE A1106 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE A1106 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 PHE A1106 " -0.020 2.00e-02 2.50e+03 pdb=" CZ PHE A1106 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 260 " -0.031 2.00e-02 2.50e+03 6.43e-02 4.14e+01 pdb=" CD GLU B 260 " 0.111 2.00e-02 2.50e+03 pdb=" OE1 GLU B 260 " -0.040 2.00e-02 2.50e+03 pdb=" OE2 GLU B 260 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 794 " 0.030 2.00e-02 2.50e+03 6.10e-02 3.72e+01 pdb=" CD GLU A 794 " -0.105 2.00e-02 2.50e+03 pdb=" OE1 GLU A 794 " 0.040 2.00e-02 2.50e+03 pdb=" OE2 GLU A 794 " 0.036 2.00e-02 2.50e+03 ... (remaining 2401 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 106 2.63 - 3.20: 12033 3.20 - 3.77: 19109 3.77 - 4.33: 27405 4.33 - 4.90: 46574 Nonbonded interactions: 105227 Sorted by model distance: nonbonded pdb=" NH1 ARG A1040 " pdb=" OE1 GLU A1246 " model vdw 2.066 3.120 nonbonded pdb=" OG1 THR A 490 " pdb=" O LYS A 517 " model vdw 2.072 3.040 nonbonded pdb=" OG SER A1191 " pdb=" OG SER A1320 " model vdw 2.164 3.040 nonbonded pdb=" OD2 ASP A1260 " pdb=" NZ LYS A1263 " model vdw 2.172 3.120 nonbonded pdb=" OE2 GLU B 260 " pdb=" NH2 ARG B 268 " model vdw 2.189 3.120 ... (remaining 105222 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 36.800 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 : 0.006 0.102 13942 Z= 0.318 Angle : 1.080 24.078 18893 Z= 0.590 Chirality : 0.060 0.567 2108 Planarity : 0.007 0.064 2404 Dihedral : 13.099 89.631 5127 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 0.13 % Allowed : 1.13 % Favored : 98.74 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 1682 helix: 0.83 (0.18), residues: 856 sheet: 0.62 (0.53), residues: 90 loop : -1.32 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1088 HIS 0.010 0.002 HIS A 669 PHE 0.098 0.004 PHE A1106 TYR 0.027 0.003 TYR A1091 ARG 0.027 0.001 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.17603 ( 684) hydrogen bonds : angle 5.92217 ( 1932) metal coordination : bond 0.00693 ( 3) covalent geometry : bond 0.00586 (13939) covalent geometry : angle 1.07959 (18893) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 292 time to evaluate : 1.485 Fit side-chains REVERT: A 9 ASP cc_start: 0.7871 (t0) cc_final: 0.6894 (p0) REVERT: A 41 ARG cc_start: 0.7974 (mmm160) cc_final: 0.7371 (mpt180) REVERT: A 44 ARG cc_start: 0.7965 (ptt-90) cc_final: 0.7731 (ptt90) REVERT: A 75 ILE cc_start: 0.7805 (mm) cc_final: 0.7278 (pt) REVERT: A 92 ASP cc_start: 0.8396 (m-30) cc_final: 0.7415 (OUTLIER) REVERT: A 95 LYS cc_start: 0.7812 (tppt) cc_final: 0.6975 (pmtt) REVERT: A 104 LYS cc_start: 0.8146 (tttp) cc_final: 0.7598 (ttmm) REVERT: A 141 LYS cc_start: 0.8078 (ttpp) cc_final: 0.7722 (mptt) REVERT: A 178 THR cc_start: 0.7952 (m) cc_final: 0.7615 (p) REVERT: A 196 LYS cc_start: 0.7064 (mptt) cc_final: 0.6820 (tmtm) REVERT: A 217 ARG cc_start: 0.7123 (ptp-110) cc_final: 0.6666 (mpt180) REVERT: A 229 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7127 (tt0) REVERT: A 245 ASP cc_start: 0.8181 (m-30) cc_final: 0.7843 (m-30) REVERT: A 278 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7500 (mm-30) REVERT: A 390 ASP cc_start: 0.7028 (m-30) cc_final: 0.6322 (t70) REVERT: A 503 ARG cc_start: 0.7148 (mtt-85) cc_final: 0.6170 (mtp-110) REVERT: A 533 GLN cc_start: 0.7559 (pp30) cc_final: 0.7008 (pp30) REVERT: A 540 LYS cc_start: 0.7738 (mmtt) cc_final: 0.7143 (mppt) REVERT: A 564 ARG cc_start: 0.8024 (mtp180) cc_final: 0.6767 (mpt180) REVERT: A 581 GLU cc_start: 0.7533 (tt0) cc_final: 0.6981 (pp20) REVERT: A 597 MET cc_start: 0.6976 (tpt) cc_final: 0.6756 (tpt) REVERT: A 677 MET cc_start: 0.9175 (mmm) cc_final: 0.8631 (mmt) REVERT: A 742 VAL cc_start: 0.7556 (t) cc_final: 0.7101 (p) REVERT: A 745 ASP cc_start: 0.5383 (t0) cc_final: 0.5079 (p0) REVERT: A 763 TYR cc_start: 0.7497 (t80) cc_final: 0.7247 (t80) REVERT: A 767 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7157 (mm-30) REVERT: A 778 GLU cc_start: 0.7730 (tp30) cc_final: 0.7294 (tp30) REVERT: A 793 GLU cc_start: 0.7613 (mm-30) cc_final: 0.6989 (mt-10) REVERT: A 794 GLU cc_start: 0.8349 (mp0) cc_final: 0.7730 (mm-30) REVERT: A 807 LYS cc_start: 0.7931 (mtmm) cc_final: 0.7577 (mttp) REVERT: A 824 ARG cc_start: 0.7580 (mtp85) cc_final: 0.6750 (mtm110) REVERT: A 895 LYS cc_start: 0.7193 (pttp) cc_final: 0.6828 (ptmt) REVERT: A 959 LYS cc_start: 0.8159 (mttt) cc_final: 0.7718 (mtmt) REVERT: A 967 ASP cc_start: 0.7940 (m-30) cc_final: 0.7533 (m-30) REVERT: A 971 ASN cc_start: 0.7654 (t0) cc_final: 0.6940 (p0) REVERT: A 1000 GLN cc_start: 0.8175 (mt0) cc_final: 0.7832 (mt0) REVERT: A 1097 ASP cc_start: 0.7624 (m-30) cc_final: 0.7010 (p0) REVERT: A 1143 GLU cc_start: 0.7978 (pt0) cc_final: 0.7081 (mm-30) REVERT: A 1155 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7712 (tp30) REVERT: A 1255 THR cc_start: 0.6198 (m) cc_final: 0.5739 (p) REVERT: A 1366 ASN cc_start: 0.8617 (p0) cc_final: 0.8334 (p0) REVERT: A 1389 ASP cc_start: 0.8126 (p0) cc_final: 0.7919 (p0) REVERT: A 1403 GLU cc_start: 0.7661 (pm20) cc_final: 0.7164 (mm-30) REVERT: B 166 LYS cc_start: 0.7862 (ttpp) cc_final: 0.7634 (tttm) REVERT: B 194 LYS cc_start: 0.7280 (mptt) cc_final: 0.6476 (pttp) REVERT: B 211 LYS cc_start: 0.7419 (tttt) cc_final: 0.7078 (tttp) REVERT: C 154 GLU cc_start: 0.8221 (tp30) cc_final: 0.7779 (tp30) REVERT: D 113 MET cc_start: 0.5435 (pmm) cc_final: 0.4565 (mtt) REVERT: E 113 MET cc_start: 0.5915 (mmp) cc_final: 0.5363 (mtp) outliers start: 2 outliers final: 1 residues processed: 294 average time/residue: 1.4512 time to fit residues: 461.9648 Evaluate side-chains 210 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 50 optimal weight: 0.0980 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 HIS A 360 GLN A 395 HIS A 509 ASN A 575 ASN A1048 GLN A1141 GLN A1158 ASN A1270 ASN A1303 HIS A1312 ASN A1322 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 = 0.3885 r_free = 0.3885 target = 0.162277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.124356 restraints weight = 15776.559| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.03 r_work: 0.3252 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13942 Z= 0.179 Angle : 0.644 9.788 18893 Z= 0.339 Chirality : 0.044 0.155 2108 Planarity : 0.005 0.048 2404 Dihedral : 4.907 30.283 1836 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.46 % Allowed : 9.51 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.20), residues: 1682 helix: 1.09 (0.18), residues: 867 sheet: 1.02 (0.52), residues: 85 loop : -1.03 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 76 HIS 0.007 0.001 HIS A 705 PHE 0.020 0.002 PHE A 372 TYR 0.022 0.002 TYR A 430 ARG 0.008 0.001 ARG A 855 Details of bonding type rmsd hydrogen bonds : bond 0.06688 ( 684) hydrogen bonds : angle 4.65028 ( 1932) metal coordination : bond 0.00193 ( 3) covalent geometry : bond 0.00421 (13939) covalent geometry : angle 0.64407 (18893) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7959 (t0) cc_final: 0.7007 (p0) REVERT: A 17 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7670 (mp) REVERT: A 41 ARG cc_start: 0.7724 (mmm160) cc_final: 0.7492 (mpt180) REVERT: A 75 ILE cc_start: 0.8032 (mm) cc_final: 0.7807 (pt) REVERT: A 92 ASP cc_start: 0.8165 (m-30) cc_final: 0.7786 (OUTLIER) REVERT: A 95 LYS cc_start: 0.8150 (tppt) cc_final: 0.7780 (pttm) REVERT: A 104 LYS cc_start: 0.8713 (tttp) cc_final: 0.8441 (ttmt) REVERT: A 196 LYS cc_start: 0.7489 (mptt) cc_final: 0.7072 (mmtm) REVERT: A 229 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7272 (tt0) REVERT: A 390 ASP cc_start: 0.7356 (m-30) cc_final: 0.7002 (t70) REVERT: A 536 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7207 (tp30) REVERT: A 540 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7739 (mppt) REVERT: A 564 ARG cc_start: 0.8356 (mtp180) cc_final: 0.7475 (mpt180) REVERT: A 603 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7774 (mm-30) REVERT: A 628 ARG cc_start: 0.8687 (tpt-90) cc_final: 0.8340 (mmt90) REVERT: A 742 VAL cc_start: 0.8247 (t) cc_final: 0.7956 (p) REVERT: A 778 GLU cc_start: 0.8382 (tp30) cc_final: 0.8132 (tp30) REVERT: A 791 LYS cc_start: 0.7837 (mtpp) cc_final: 0.7468 (tttp) REVERT: A 794 GLU cc_start: 0.8226 (mp0) cc_final: 0.7965 (mp0) REVERT: A 824 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7357 (mtm-85) REVERT: A 869 MET cc_start: 0.8493 (tpt) cc_final: 0.8122 (tpt) REVERT: A 895 LYS cc_start: 0.7835 (pttp) cc_final: 0.7526 (ptmt) REVERT: A 959 LYS cc_start: 0.8136 (mttt) cc_final: 0.7723 (mtmt) REVERT: A 1000 GLN cc_start: 0.8187 (mt0) cc_final: 0.7929 (mt0) REVERT: A 1097 ASP cc_start: 0.7556 (m-30) cc_final: 0.7220 (p0) REVERT: A 1104 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7013 (mp0) REVERT: A 1143 GLU cc_start: 0.7986 (pt0) cc_final: 0.7657 (mt-10) REVERT: A 1155 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7937 (tp30) REVERT: A 1255 THR cc_start: 0.5993 (m) cc_final: 0.5721 (p) REVERT: A 1366 ASN cc_start: 0.8549 (p0) cc_final: 0.8332 (p0) REVERT: A 1374 ASN cc_start: 0.8022 (m-40) cc_final: 0.7618 (m110) REVERT: A 1401 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7250 (p0) REVERT: B 194 LYS cc_start: 0.7891 (mptt) cc_final: 0.7366 (ttpp) REVERT: C 113 MET cc_start: 0.3476 (ppp) cc_final: 0.3161 (ptp) REVERT: C 154 GLU cc_start: 0.8230 (tp30) cc_final: 0.7953 (tp30) outliers start: 37 outliers final: 16 residues processed: 237 average time/residue: 1.3243 time to fit residues: 342.6107 Evaluate side-chains 209 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1337 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1401 ASP Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 113 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 89 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 GLN A1158 ASN A1270 ASN A1322 ASN A1338 ASN C 161 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.163319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.125549 restraints weight = 15768.196| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.03 r_work: 0.3251 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13942 Z= 0.131 Angle : 0.540 8.719 18893 Z= 0.284 Chirality : 0.041 0.155 2108 Planarity : 0.004 0.047 2404 Dihedral : 4.489 26.888 1836 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.73 % Allowed : 11.97 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.20), residues: 1682 helix: 1.43 (0.18), residues: 867 sheet: 1.23 (0.49), residues: 90 loop : -0.91 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.005 0.001 HIS A 154 PHE 0.015 0.002 PHE A 372 TYR 0.014 0.001 TYR A 116 ARG 0.006 0.000 ARG A 855 Details of bonding type rmsd hydrogen bonds : bond 0.05420 ( 684) hydrogen bonds : angle 4.23231 ( 1932) metal coordination : bond 0.00106 ( 3) covalent geometry : bond 0.00297 (13939) covalent geometry : angle 0.54046 (18893) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8021 (t0) cc_final: 0.6917 (p0) REVERT: A 41 ARG cc_start: 0.7677 (mmm160) cc_final: 0.7343 (mpt180) REVERT: A 92 ASP cc_start: 0.8092 (m-30) cc_final: 0.7682 (t70) REVERT: A 95 LYS cc_start: 0.8186 (tppt) cc_final: 0.7796 (pttm) REVERT: A 123 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8445 (mt) REVERT: A 196 LYS cc_start: 0.7494 (mptt) cc_final: 0.6989 (mmtm) REVERT: A 229 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7079 (tt0) REVERT: A 289 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7786 (ttm) REVERT: A 390 ASP cc_start: 0.7420 (m-30) cc_final: 0.7039 (t70) REVERT: A 426 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7224 (mt0) REVERT: A 536 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6901 (tp30) REVERT: A 540 LYS cc_start: 0.7891 (mmtt) cc_final: 0.7650 (mppt) REVERT: A 564 ARG cc_start: 0.8412 (mtp180) cc_final: 0.8051 (mtm180) REVERT: A 581 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7169 (tp30) REVERT: A 628 ARG cc_start: 0.8599 (tpt-90) cc_final: 0.8325 (mmt90) REVERT: A 693 ASN cc_start: 0.6775 (t0) cc_final: 0.6573 (t0) REVERT: A 742 VAL cc_start: 0.8121 (t) cc_final: 0.7883 (p) REVERT: A 778 GLU cc_start: 0.8359 (tp30) cc_final: 0.8025 (tp30) REVERT: A 785 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.8247 (m-80) REVERT: A 794 GLU cc_start: 0.8199 (mp0) cc_final: 0.7850 (mp0) REVERT: A 824 ARG cc_start: 0.7931 (mtp85) cc_final: 0.7378 (mtm180) REVERT: A 832 ILE cc_start: 0.7678 (mt) cc_final: 0.7359 (mm) REVERT: A 894 LYS cc_start: 0.8752 (mtpp) cc_final: 0.8337 (mmtt) REVERT: A 895 LYS cc_start: 0.7591 (pttp) cc_final: 0.7263 (ptmt) REVERT: A 959 LYS cc_start: 0.8101 (mttt) cc_final: 0.7657 (mtmt) REVERT: A 1000 GLN cc_start: 0.8158 (mt0) cc_final: 0.7842 (mt0) REVERT: A 1040 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7388 (mtt-85) REVERT: A 1104 GLU cc_start: 0.7459 (mm-30) cc_final: 0.6959 (mt-10) REVERT: A 1155 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7842 (tp30) REVERT: A 1306 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7551 (ppp) REVERT: A 1385 TYR cc_start: 0.7512 (m-80) cc_final: 0.7248 (m-10) REVERT: A 1387 TYR cc_start: 0.8140 (t80) cc_final: 0.7825 (t80) REVERT: B 194 LYS cc_start: 0.7903 (mptt) cc_final: 0.7321 (ttpp) REVERT: C 113 MET cc_start: 0.3367 (ppp) cc_final: 0.3077 (ptp) REVERT: C 127 MET cc_start: 0.7065 (mmt) cc_final: 0.6296 (mmp) REVERT: C 154 GLU cc_start: 0.8285 (tp30) cc_final: 0.7853 (tp30) outliers start: 41 outliers final: 16 residues processed: 224 average time/residue: 1.2534 time to fit residues: 307.7854 Evaluate side-chains 207 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1188 ASN Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1306 MET Chi-restraints excluded: chain A residue 1337 SER Chi-restraints excluded: chain C residue 135 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 90 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 145 optimal weight: 8.9990 chunk 164 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN A 994 ASN A1048 GLN A1158 ASN A1256 GLN A1270 ASN A1287 HIS A1322 ASN A1374 ASN C 161 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.159061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.121219 restraints weight = 15733.962| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.99 r_work: 0.3186 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13942 Z= 0.211 Angle : 0.621 9.880 18893 Z= 0.324 Chirality : 0.044 0.156 2108 Planarity : 0.005 0.050 2404 Dihedral : 4.736 30.431 1836 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.72 % Allowed : 12.30 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.20), residues: 1682 helix: 1.21 (0.18), residues: 866 sheet: 1.31 (0.51), residues: 91 loop : -0.95 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 108 HIS 0.007 0.001 HIS A 154 PHE 0.023 0.002 PHE A 414 TYR 0.022 0.002 TYR A 803 ARG 0.005 0.000 ARG A 855 Details of bonding type rmsd hydrogen bonds : bond 0.07055 ( 684) hydrogen bonds : angle 4.37924 ( 1932) metal coordination : bond 0.00399 ( 3) covalent geometry : bond 0.00523 (13939) covalent geometry : angle 0.62134 (18893) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 188 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7689 (mp) REVERT: A 41 ARG cc_start: 0.7786 (mmm160) cc_final: 0.7370 (mmt180) REVERT: A 51 ARG cc_start: 0.8283 (ptm160) cc_final: 0.7734 (ptt-90) REVERT: A 196 LYS cc_start: 0.7419 (mptt) cc_final: 0.6946 (mmtm) REVERT: A 217 ARG cc_start: 0.7418 (mpt180) cc_final: 0.7164 (mpt180) REVERT: A 229 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6984 (tt0) REVERT: A 289 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7960 (ttm) REVERT: A 390 ASP cc_start: 0.7418 (m-30) cc_final: 0.7055 (t70) REVERT: A 521 GLU cc_start: 0.7041 (mp0) cc_final: 0.6824 (mp0) REVERT: A 536 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7236 (tp30) REVERT: A 540 LYS cc_start: 0.8101 (mmtt) cc_final: 0.7886 (mppt) REVERT: A 564 ARG cc_start: 0.8466 (mtp180) cc_final: 0.8131 (mtm180) REVERT: A 581 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7182 (tp30) REVERT: A 605 LYS cc_start: 0.6604 (mtpm) cc_final: 0.6356 (mmmt) REVERT: A 628 ARG cc_start: 0.8670 (tpt-90) cc_final: 0.8384 (mmt90) REVERT: A 696 ASN cc_start: 0.7667 (t0) cc_final: 0.7299 (m-40) REVERT: A 770 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7713 (mp) REVERT: A 778 GLU cc_start: 0.8427 (tp30) cc_final: 0.8134 (tp30) REVERT: A 785 TYR cc_start: 0.9116 (OUTLIER) cc_final: 0.8315 (m-80) REVERT: A 791 LYS cc_start: 0.7777 (mtpp) cc_final: 0.7482 (mtpp) REVERT: A 794 GLU cc_start: 0.8374 (mp0) cc_final: 0.8116 (mp0) REVERT: A 820 LYS cc_start: 0.8968 (ptmm) cc_final: 0.8711 (ptmm) REVERT: A 824 ARG cc_start: 0.8019 (mtp85) cc_final: 0.7389 (mtm180) REVERT: A 894 LYS cc_start: 0.8808 (mtpp) cc_final: 0.8351 (mmtt) REVERT: A 895 LYS cc_start: 0.7598 (pttp) cc_final: 0.7301 (ptmt) REVERT: A 927 ASN cc_start: 0.8657 (m110) cc_final: 0.8277 (m-40) REVERT: A 959 LYS cc_start: 0.8076 (mttt) cc_final: 0.7664 (mtmt) REVERT: A 962 LEU cc_start: 0.7577 (mt) cc_final: 0.7316 (pp) REVERT: A 1040 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.7605 (mtt-85) REVERT: A 1073 MET cc_start: 0.6854 (tpt) cc_final: 0.6593 (tpt) REVERT: A 1104 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7043 (mt-10) REVERT: A 1143 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7618 (pt0) REVERT: A 1155 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7856 (tp30) REVERT: A 1385 TYR cc_start: 0.7442 (m-80) cc_final: 0.7161 (m-10) REVERT: B 194 LYS cc_start: 0.7894 (mptt) cc_final: 0.7326 (ttpp) REVERT: B 260 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7701 (mt-10) REVERT: C 113 MET cc_start: 0.3578 (ppp) cc_final: 0.3242 (ptp) REVERT: C 127 MET cc_start: 0.6992 (mmt) cc_final: 0.6281 (mmp) REVERT: C 154 GLU cc_start: 0.8323 (tp30) cc_final: 0.7900 (tp30) outliers start: 56 outliers final: 27 residues processed: 220 average time/residue: 1.3073 time to fit residues: 313.7536 Evaluate side-chains 213 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 877 GLN Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1109 THR Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1188 ASN Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 113 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 144 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 166 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 125 optimal weight: 0.0270 chunk 51 optimal weight: 0.4980 chunk 120 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 overall best weight: 3.1044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 ASN ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 994 ASN A1048 GLN A1158 ASN A1322 ASN A1374 ASN C 161 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.158573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.120862 restraints weight = 15750.861| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.00 r_work: 0.3181 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13942 Z= 0.212 Angle : 0.614 10.304 18893 Z= 0.320 Chirality : 0.044 0.161 2108 Planarity : 0.005 0.052 2404 Dihedral : 4.738 30.521 1836 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.52 % Allowed : 14.43 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.20), residues: 1682 helix: 1.07 (0.18), residues: 874 sheet: 1.13 (0.50), residues: 97 loop : -0.99 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 108 HIS 0.007 0.001 HIS A 154 PHE 0.023 0.002 PHE A 414 TYR 0.020 0.002 TYR A 803 ARG 0.004 0.000 ARG A 855 Details of bonding type rmsd hydrogen bonds : bond 0.06787 ( 684) hydrogen bonds : angle 4.37089 ( 1932) metal coordination : bond 0.00424 ( 3) covalent geometry : bond 0.00524 (13939) covalent geometry : angle 0.61389 (18893) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 179 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7710 (mp) REVERT: A 41 ARG cc_start: 0.7811 (mmm160) cc_final: 0.7374 (mmt180) REVERT: A 51 ARG cc_start: 0.8278 (ptm160) cc_final: 0.7778 (ptt-90) REVERT: A 196 LYS cc_start: 0.7448 (mptt) cc_final: 0.6941 (mmtm) REVERT: A 229 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7006 (tt0) REVERT: A 289 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7886 (ttm) REVERT: A 390 ASP cc_start: 0.7483 (m-30) cc_final: 0.7127 (t70) REVERT: A 536 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7324 (tp30) REVERT: A 542 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8093 (mm-30) REVERT: A 581 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7174 (tp30) REVERT: A 605 LYS cc_start: 0.6643 (mtpm) cc_final: 0.6382 (mmmt) REVERT: A 628 ARG cc_start: 0.8680 (tpt-90) cc_final: 0.8469 (mmt90) REVERT: A 696 ASN cc_start: 0.7748 (t0) cc_final: 0.7352 (m110) REVERT: A 770 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7700 (mp) REVERT: A 785 TYR cc_start: 0.9123 (OUTLIER) cc_final: 0.8471 (m-80) REVERT: A 794 GLU cc_start: 0.8403 (mp0) cc_final: 0.8172 (mp0) REVERT: A 824 ARG cc_start: 0.8075 (mtp85) cc_final: 0.7363 (mtm180) REVERT: A 894 LYS cc_start: 0.8836 (mtpp) cc_final: 0.8407 (mmtt) REVERT: A 895 LYS cc_start: 0.7583 (pttp) cc_final: 0.7291 (ptmt) REVERT: A 925 TYR cc_start: 0.9115 (OUTLIER) cc_final: 0.8019 (p90) REVERT: A 927 ASN cc_start: 0.8654 (m110) cc_final: 0.8308 (m-40) REVERT: A 959 LYS cc_start: 0.8024 (mttt) cc_final: 0.7609 (mtmt) REVERT: A 1040 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7648 (mtt-85) REVERT: A 1073 MET cc_start: 0.6890 (tpt) cc_final: 0.6612 (tpt) REVERT: A 1104 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7051 (mt-10) REVERT: A 1143 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7567 (pt0) REVERT: A 1155 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7863 (tp30) REVERT: A 1403 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6933 (pt0) REVERT: B 194 LYS cc_start: 0.7878 (mptt) cc_final: 0.7320 (ttpp) REVERT: B 260 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: C 113 MET cc_start: 0.3598 (ppp) cc_final: 0.3271 (ptp) REVERT: C 154 GLU cc_start: 0.8271 (tp30) cc_final: 0.7946 (tp30) outliers start: 53 outliers final: 28 residues processed: 212 average time/residue: 1.3772 time to fit residues: 318.4488 Evaluate side-chains 208 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 877 GLN Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 925 TYR Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1109 THR Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1188 ASN Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 113 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 22 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 163 optimal weight: 0.0370 chunk 35 optimal weight: 3.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 GLN A1158 ASN A1322 ASN C 161 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.162095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.124570 restraints weight = 15832.749| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.03 r_work: 0.3238 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13942 Z= 0.124 Angle : 0.525 8.766 18893 Z= 0.274 Chirality : 0.040 0.159 2108 Planarity : 0.004 0.050 2404 Dihedral : 4.409 28.536 1836 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.12 % Allowed : 15.56 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.20), residues: 1682 helix: 1.46 (0.18), residues: 871 sheet: 1.18 (0.50), residues: 97 loop : -0.89 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 76 HIS 0.005 0.001 HIS A 154 PHE 0.017 0.001 PHE A 414 TYR 0.016 0.001 TYR A 803 ARG 0.003 0.000 ARG A 518 Details of bonding type rmsd hydrogen bonds : bond 0.05117 ( 684) hydrogen bonds : angle 4.15376 ( 1932) metal coordination : bond 0.00118 ( 3) covalent geometry : bond 0.00281 (13939) covalent geometry : angle 0.52485 (18893) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7602 (mp) REVERT: A 41 ARG cc_start: 0.7797 (mmm160) cc_final: 0.7358 (mmt180) REVERT: A 51 ARG cc_start: 0.8269 (ptm160) cc_final: 0.7783 (ptt-90) REVERT: A 196 LYS cc_start: 0.7505 (mptt) cc_final: 0.6986 (mmtm) REVERT: A 229 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7029 (tt0) REVERT: A 431 LYS cc_start: 0.7619 (tptp) cc_final: 0.7249 (mptt) REVERT: A 536 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7288 (tp30) REVERT: A 542 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8064 (mm-30) REVERT: A 581 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7177 (tp30) REVERT: A 696 ASN cc_start: 0.7670 (t0) cc_final: 0.7415 (m110) REVERT: A 778 GLU cc_start: 0.8501 (tp30) cc_final: 0.8185 (tp30) REVERT: A 791 LYS cc_start: 0.7659 (mtpp) cc_final: 0.7127 (mttt) REVERT: A 824 ARG cc_start: 0.7981 (mtp85) cc_final: 0.7340 (mtm180) REVERT: A 895 LYS cc_start: 0.7493 (pttp) cc_final: 0.7156 (ptmt) REVERT: A 925 TYR cc_start: 0.9099 (OUTLIER) cc_final: 0.7887 (p90) REVERT: A 927 ASN cc_start: 0.8599 (m110) cc_final: 0.8237 (m-40) REVERT: A 959 LYS cc_start: 0.8048 (mttt) cc_final: 0.7623 (mtmt) REVERT: A 962 LEU cc_start: 0.7574 (mt) cc_final: 0.7330 (pp) REVERT: A 1040 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.7651 (mtt-85) REVERT: A 1073 MET cc_start: 0.6727 (tpt) cc_final: 0.6436 (tpt) REVERT: A 1104 GLU cc_start: 0.7571 (mm-30) cc_final: 0.6999 (mt-10) REVERT: A 1143 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: A 1155 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7851 (tp30) REVERT: B 194 LYS cc_start: 0.7857 (mptt) cc_final: 0.7259 (ttpp) REVERT: B 260 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: C 113 MET cc_start: 0.3716 (ppp) cc_final: 0.3367 (ptp) REVERT: C 124 MET cc_start: 0.6208 (ttp) cc_final: 0.5978 (ttm) REVERT: C 154 GLU cc_start: 0.8242 (tp30) cc_final: 0.7957 (tp30) outliers start: 47 outliers final: 21 residues processed: 212 average time/residue: 1.2071 time to fit residues: 280.9965 Evaluate side-chains 198 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 925 TYR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 995 ILE Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1109 THR Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 113 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 71 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 13 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS A 693 ASN ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 GLN A1048 GLN C 161 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.163663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126028 restraints weight = 15725.821| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.99 r_work: 0.3267 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13942 Z= 0.107 Angle : 0.502 8.366 18893 Z= 0.260 Chirality : 0.040 0.156 2108 Planarity : 0.004 0.050 2404 Dihedral : 4.169 26.331 1836 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.86 % Allowed : 16.09 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.21), residues: 1682 helix: 1.66 (0.18), residues: 873 sheet: 1.21 (0.49), residues: 97 loop : -0.77 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 76 HIS 0.003 0.001 HIS A 154 PHE 0.015 0.001 PHE A 414 TYR 0.015 0.001 TYR A 237 ARG 0.004 0.000 ARG A1057 Details of bonding type rmsd hydrogen bonds : bond 0.04472 ( 684) hydrogen bonds : angle 4.04347 ( 1932) metal coordination : bond 0.00124 ( 3) covalent geometry : bond 0.00231 (13939) covalent geometry : angle 0.50245 (18893) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 173 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.7755 (mmm160) cc_final: 0.7332 (mmt180) REVERT: A 51 ARG cc_start: 0.8210 (ptm160) cc_final: 0.7715 (ptt-90) REVERT: A 196 LYS cc_start: 0.7451 (mptt) cc_final: 0.6924 (mmtm) REVERT: A 217 ARG cc_start: 0.7410 (mpt180) cc_final: 0.7201 (mpt180) REVERT: A 229 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7034 (tt0) REVERT: A 431 LYS cc_start: 0.7635 (tptp) cc_final: 0.7287 (mptt) REVERT: A 536 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7241 (tp30) REVERT: A 542 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8061 (mm-30) REVERT: A 581 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7182 (tp30) REVERT: A 696 ASN cc_start: 0.7608 (t0) cc_final: 0.7375 (m110) REVERT: A 770 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7702 (mp) REVERT: A 778 GLU cc_start: 0.8479 (tp30) cc_final: 0.8169 (tp30) REVERT: A 791 LYS cc_start: 0.7589 (mtpp) cc_final: 0.7370 (mtpp) REVERT: A 822 MET cc_start: 0.9052 (tpt) cc_final: 0.8809 (tpt) REVERT: A 824 ARG cc_start: 0.7973 (mtp85) cc_final: 0.7334 (mtm180) REVERT: A 895 LYS cc_start: 0.7373 (pttp) cc_final: 0.7049 (ptmt) REVERT: A 925 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.7847 (p90) REVERT: A 927 ASN cc_start: 0.8567 (m110) cc_final: 0.8194 (m-40) REVERT: A 959 LYS cc_start: 0.8067 (mttt) cc_final: 0.7618 (mtmt) REVERT: A 962 LEU cc_start: 0.7596 (mt) cc_final: 0.7355 (pp) REVERT: A 1104 GLU cc_start: 0.7534 (mm-30) cc_final: 0.6977 (mt-10) REVERT: A 1143 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: A 1155 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7857 (tp30) REVERT: B 194 LYS cc_start: 0.7898 (mptt) cc_final: 0.7282 (ttpp) REVERT: B 260 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7632 (mt-10) REVERT: C 113 MET cc_start: 0.3577 (ppp) cc_final: 0.3218 (ptp) REVERT: C 124 MET cc_start: 0.6076 (ttp) cc_final: 0.5871 (ttm) REVERT: C 154 GLU cc_start: 0.8251 (tp30) cc_final: 0.7858 (tp30) outliers start: 43 outliers final: 21 residues processed: 201 average time/residue: 1.3017 time to fit residues: 286.7846 Evaluate side-chains 196 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 925 TYR Chi-restraints excluded: chain A residue 995 ILE Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1109 THR Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 134 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 104 optimal weight: 0.0870 chunk 125 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 GLN A1158 ASN A1270 ASN B 254 GLN C 161 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.162210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.124529 restraints weight = 15662.116| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.99 r_work: 0.3245 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13942 Z= 0.127 Angle : 0.523 9.723 18893 Z= 0.270 Chirality : 0.040 0.155 2108 Planarity : 0.004 0.050 2404 Dihedral : 4.187 27.331 1836 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.73 % Allowed : 16.49 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1682 helix: 1.62 (0.18), residues: 873 sheet: 1.16 (0.49), residues: 97 loop : -0.78 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.005 0.001 HIS A 154 PHE 0.018 0.001 PHE A 414 TYR 0.015 0.001 TYR A 803 ARG 0.005 0.000 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.05027 ( 684) hydrogen bonds : angle 4.07604 ( 1932) metal coordination : bond 0.00181 ( 3) covalent geometry : bond 0.00296 (13939) covalent geometry : angle 0.52295 (18893) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.7750 (mmm160) cc_final: 0.7324 (mmt180) REVERT: A 51 ARG cc_start: 0.8216 (ptm160) cc_final: 0.7710 (ptt-90) REVERT: A 141 LYS cc_start: 0.8362 (mptt) cc_final: 0.8143 (mptm) REVERT: A 196 LYS cc_start: 0.7449 (mptt) cc_final: 0.6919 (mmtm) REVERT: A 229 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7012 (tt0) REVERT: A 289 MET cc_start: 0.8449 (tpp) cc_final: 0.8178 (tpt) REVERT: A 431 LYS cc_start: 0.7638 (tptp) cc_final: 0.7269 (mptt) REVERT: A 536 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7251 (tp30) REVERT: A 542 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8054 (mm-30) REVERT: A 581 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7203 (tp30) REVERT: A 605 LYS cc_start: 0.6623 (mtpm) cc_final: 0.6349 (mmmt) REVERT: A 696 ASN cc_start: 0.7624 (t0) cc_final: 0.7363 (m110) REVERT: A 770 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7658 (mp) REVERT: A 778 GLU cc_start: 0.8473 (tp30) cc_final: 0.8163 (tp30) REVERT: A 824 ARG cc_start: 0.7986 (mtp85) cc_final: 0.7318 (mtm180) REVERT: A 895 LYS cc_start: 0.7357 (pttp) cc_final: 0.7033 (ptmt) REVERT: A 925 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.7851 (p90) REVERT: A 927 ASN cc_start: 0.8573 (m110) cc_final: 0.8198 (m-40) REVERT: A 959 LYS cc_start: 0.8056 (mttt) cc_final: 0.7589 (mtmt) REVERT: A 962 LEU cc_start: 0.7605 (mt) cc_final: 0.7372 (pp) REVERT: A 1073 MET cc_start: 0.6603 (tpt) cc_final: 0.6367 (tpt) REVERT: A 1104 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6985 (mt-10) REVERT: A 1143 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: A 1155 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7839 (tp30) REVERT: B 194 LYS cc_start: 0.7871 (mptt) cc_final: 0.7302 (ttpp) REVERT: B 260 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: C 113 MET cc_start: 0.3537 (ppp) cc_final: 0.3178 (ptp) REVERT: C 124 MET cc_start: 0.6018 (ttp) cc_final: 0.5812 (ttm) REVERT: C 154 GLU cc_start: 0.8252 (tp30) cc_final: 0.7848 (tp30) outliers start: 41 outliers final: 27 residues processed: 204 average time/residue: 1.3091 time to fit residues: 293.8993 Evaluate side-chains 204 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 925 TYR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 995 ILE Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1109 THR Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 134 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 6 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 166 optimal weight: 20.0000 chunk 95 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 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 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 GLN C 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.158039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.120399 restraints weight = 15736.804| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.99 r_work: 0.3199 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13942 Z= 0.230 Angle : 0.630 12.502 18893 Z= 0.324 Chirality : 0.045 0.155 2108 Planarity : 0.005 0.052 2404 Dihedral : 4.603 31.122 1836 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.86 % Allowed : 16.76 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1682 helix: 1.24 (0.18), residues: 872 sheet: 1.04 (0.49), residues: 97 loop : -0.90 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 108 HIS 0.006 0.001 HIS A 154 PHE 0.026 0.002 PHE A 414 TYR 0.020 0.002 TYR A 803 ARG 0.006 0.001 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.07111 ( 684) hydrogen bonds : angle 4.33435 ( 1932) metal coordination : bond 0.00738 ( 3) covalent geometry : bond 0.00570 (13939) covalent geometry : angle 0.63014 (18893) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.7811 (mp) REVERT: A 41 ARG cc_start: 0.7809 (mmm160) cc_final: 0.7425 (mmt180) REVERT: A 51 ARG cc_start: 0.8284 (ptm160) cc_final: 0.7817 (ptt-90) REVERT: A 141 LYS cc_start: 0.8536 (mptt) cc_final: 0.8335 (mptm) REVERT: A 196 LYS cc_start: 0.7606 (mptt) cc_final: 0.7156 (mmtm) REVERT: A 289 MET cc_start: 0.8655 (tpp) cc_final: 0.8243 (tpt) REVERT: A 390 ASP cc_start: 0.7557 (m-30) cc_final: 0.7281 (t70) REVERT: A 431 LYS cc_start: 0.7751 (tptp) cc_final: 0.7431 (mptt) REVERT: A 536 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7465 (tp30) REVERT: A 542 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8171 (mm-30) REVERT: A 564 ARG cc_start: 0.8438 (mmm-85) cc_final: 0.8230 (mmm-85) REVERT: A 581 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7309 (tp30) REVERT: A 605 LYS cc_start: 0.6727 (mtpm) cc_final: 0.6443 (mmmt) REVERT: A 696 ASN cc_start: 0.7800 (t0) cc_final: 0.7419 (m110) REVERT: A 770 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7846 (mp) REVERT: A 778 GLU cc_start: 0.8552 (tp30) cc_final: 0.8194 (tp30) REVERT: A 785 TYR cc_start: 0.9147 (OUTLIER) cc_final: 0.8526 (m-80) REVERT: A 824 ARG cc_start: 0.8094 (mtp85) cc_final: 0.7481 (mtm180) REVERT: A 895 LYS cc_start: 0.7545 (pttp) cc_final: 0.7228 (ptmt) REVERT: A 925 TYR cc_start: 0.9131 (OUTLIER) cc_final: 0.7913 (p90) REVERT: A 927 ASN cc_start: 0.8641 (m110) cc_final: 0.8352 (m-40) REVERT: A 959 LYS cc_start: 0.8036 (mttt) cc_final: 0.7630 (mtmt) REVERT: A 1104 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7161 (mt-10) REVERT: B 194 LYS cc_start: 0.8019 (mptt) cc_final: 0.7516 (ttpp) REVERT: B 254 GLN cc_start: 0.8523 (tt0) cc_final: 0.8319 (tt0) REVERT: C 113 MET cc_start: 0.3667 (ppp) cc_final: 0.3324 (ptp) REVERT: C 124 MET cc_start: 0.6161 (ttp) cc_final: 0.5931 (ttm) REVERT: C 154 GLU cc_start: 0.8281 (tp30) cc_final: 0.7880 (tp30) outliers start: 43 outliers final: 23 residues processed: 197 average time/residue: 1.3143 time to fit residues: 284.1260 Evaluate side-chains 194 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 925 TYR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 992 ARG Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1109 THR Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 113 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 153 optimal weight: 20.0000 chunk 106 optimal weight: 0.6980 chunk 105 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 GLN C 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.161707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.124493 restraints weight = 15617.858| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.95 r_work: 0.3238 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13942 Z= 0.125 Angle : 0.540 12.675 18893 Z= 0.277 Chirality : 0.040 0.134 2108 Planarity : 0.004 0.049 2404 Dihedral : 4.328 28.683 1836 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.93 % Allowed : 17.55 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 1682 helix: 1.54 (0.18), residues: 868 sheet: 1.14 (0.50), residues: 97 loop : -0.87 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 76 HIS 0.004 0.001 HIS A 154 PHE 0.018 0.001 PHE A 414 TYR 0.015 0.001 TYR A 803 ARG 0.005 0.000 ARG A 628 Details of bonding type rmsd hydrogen bonds : bond 0.05109 ( 684) hydrogen bonds : angle 4.17189 ( 1932) metal coordination : bond 0.00175 ( 3) covalent geometry : bond 0.00288 (13939) covalent geometry : angle 0.53997 (18893) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.7712 (mmm160) cc_final: 0.7298 (mmt180) REVERT: A 51 ARG cc_start: 0.8206 (ptm160) cc_final: 0.7698 (ptt-90) REVERT: A 141 LYS cc_start: 0.8405 (mptt) cc_final: 0.8185 (mptm) REVERT: A 196 LYS cc_start: 0.7482 (mptt) cc_final: 0.7013 (mmtm) REVERT: A 289 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8134 (tpt) REVERT: A 431 LYS cc_start: 0.7671 (tptp) cc_final: 0.7336 (mptt) REVERT: A 536 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7278 (tp30) REVERT: A 542 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8066 (mm-30) REVERT: A 564 ARG cc_start: 0.8331 (mmm-85) cc_final: 0.8118 (mmm-85) REVERT: A 581 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7193 (tp30) REVERT: A 696 ASN cc_start: 0.7732 (t0) cc_final: 0.7398 (m110) REVERT: A 778 GLU cc_start: 0.8434 (tp30) cc_final: 0.8046 (tp30) REVERT: A 791 LYS cc_start: 0.7921 (mtpp) cc_final: 0.7328 (mttt) REVERT: A 824 ARG cc_start: 0.8009 (mtp85) cc_final: 0.7345 (mtm180) REVERT: A 895 LYS cc_start: 0.7354 (pttp) cc_final: 0.7030 (ptmt) REVERT: A 925 TYR cc_start: 0.9132 (OUTLIER) cc_final: 0.7897 (p90) REVERT: A 927 ASN cc_start: 0.8542 (m110) cc_final: 0.8194 (m-40) REVERT: A 959 LYS cc_start: 0.8040 (mttt) cc_final: 0.7587 (mtmt) REVERT: A 1073 MET cc_start: 0.6712 (tpt) cc_final: 0.6500 (tpt) REVERT: A 1104 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7011 (mt-10) REVERT: A 1143 GLU cc_start: 0.7843 (pt0) cc_final: 0.7397 (mt-10) REVERT: A 1246 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7085 (mm-30) REVERT: B 194 LYS cc_start: 0.7908 (mptt) cc_final: 0.7309 (ttpp) REVERT: C 113 MET cc_start: 0.3552 (ppp) cc_final: 0.3218 (ptp) REVERT: C 124 MET cc_start: 0.5984 (ttp) cc_final: 0.5768 (ttm) REVERT: C 154 GLU cc_start: 0.8237 (tp30) cc_final: 0.7839 (tp30) outliers start: 29 outliers final: 19 residues processed: 182 average time/residue: 1.2995 time to fit residues: 259.1447 Evaluate side-chains 184 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 925 TYR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 992 ARG Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1109 THR Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 113 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 82 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 GLN A1158 ASN C 161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.160501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.123140 restraints weight = 15839.689| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.99 r_work: 0.3241 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13942 Z= 0.153 Angle : 0.565 13.697 18893 Z= 0.289 Chirality : 0.041 0.135 2108 Planarity : 0.004 0.051 2404 Dihedral : 4.347 28.939 1836 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.13 % Allowed : 17.35 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1682 helix: 1.49 (0.18), residues: 867 sheet: 1.11 (0.49), residues: 97 loop : -0.87 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 108 HIS 0.005 0.001 HIS A 154 PHE 0.021 0.002 PHE A 414 TYR 0.017 0.001 TYR A 803 ARG 0.005 0.000 ARG A 628 Details of bonding type rmsd hydrogen bonds : bond 0.05687 ( 684) hydrogen bonds : angle 4.20472 ( 1932) metal coordination : bond 0.00294 ( 3) covalent geometry : bond 0.00367 (13939) covalent geometry : angle 0.56472 (18893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10576.72 seconds wall clock time: 180 minutes 47.88 seconds (10847.88 seconds total)