Starting phenix.real_space_refine on Thu Sep 18 03:09:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ip4_60757/09_2025/9ip4_60757.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ip4_60757/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ip4_60757/09_2025/9ip4_60757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ip4_60757/09_2025/9ip4_60757.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ip4_60757/09_2025/9ip4_60757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ip4_60757/09_2025/9ip4_60757.map" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.044 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.08, per 1000 atoms: 0.23 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: 1.02 Conformation dependent library (CDL) restraints added in 486.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.46 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: 2.13 Time building geometry restraints manager: 1.40 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.090 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.340 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (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 ARG 0.027 0.001 ARG A 217 TYR 0.027 0.003 TYR A1091 PHE 0.098 0.004 PHE A1106 TRP 0.027 0.002 TRP A1088 HIS 0.010 0.002 HIS A 669 Details of bonding type rmsd covalent geometry : bond 0.00586 (13939) covalent geometry : angle 1.07959 (18893) hydrogen bonds : bond 0.17603 ( 684) hydrogen bonds : angle 5.92217 ( 1932) metal coordination : bond 0.00693 ( 3) *********************** 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 : 0.528 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: 0.6425 time to fit residues: 203.7844 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 : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0270 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.5444 ------------------------------------------------------------------------------- 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 A1287 HIS A1303 HIS A1312 ASN A1322 ASN C 161 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.161431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.123429 restraints weight = 15800.401| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.02 r_work: 0.3241 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13942 Z= 0.200 Angle : 0.668 10.138 18893 Z= 0.350 Chirality : 0.045 0.154 2108 Planarity : 0.005 0.048 2404 Dihedral : 4.963 30.611 1836 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.59 % Allowed : 9.44 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.20), residues: 1682 helix: 1.03 (0.18), residues: 866 sheet: 1.05 (0.53), residues: 85 loop : -1.06 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 855 TYR 0.025 0.002 TYR A 430 PHE 0.021 0.002 PHE A 372 TRP 0.009 0.002 TRP A1210 HIS 0.008 0.001 HIS A 705 Details of bonding type rmsd covalent geometry : bond 0.00481 (13939) covalent geometry : angle 0.66800 (18893) hydrogen bonds : bond 0.06909 ( 684) hydrogen bonds : angle 4.66542 ( 1932) metal coordination : bond 0.00161 ( 3) *********************** 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 260 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 221 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7994 (t0) cc_final: 0.7044 (p0) REVERT: A 17 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7714 (mp) REVERT: A 41 ARG cc_start: 0.7757 (mmm160) cc_final: 0.7478 (mpt180) REVERT: A 75 ILE cc_start: 0.8092 (mm) cc_final: 0.7853 (pt) REVERT: A 92 ASP cc_start: 0.8129 (m-30) cc_final: 0.7767 (t70) REVERT: A 95 LYS cc_start: 0.8153 (tppt) cc_final: 0.7818 (pttm) REVERT: A 196 LYS cc_start: 0.7517 (mptt) cc_final: 0.7104 (mmtm) REVERT: A 229 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7281 (tt0) REVERT: A 390 ASP cc_start: 0.7414 (m-30) cc_final: 0.7053 (t70) REVERT: A 536 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7238 (tp30) REVERT: A 540 LYS cc_start: 0.8040 (mmtt) cc_final: 0.7839 (mppt) REVERT: A 564 ARG cc_start: 0.8324 (mtp180) cc_final: 0.7455 (mpt180) REVERT: A 628 ARG cc_start: 0.8707 (tpt-90) cc_final: 0.8366 (mmt90) REVERT: A 742 VAL cc_start: 0.8271 (t) cc_final: 0.7990 (p) REVERT: A 791 LYS cc_start: 0.7869 (mtpp) cc_final: 0.7494 (tttp) REVERT: A 794 GLU cc_start: 0.8211 (mp0) cc_final: 0.7985 (mp0) REVERT: A 824 ARG cc_start: 0.7892 (mtp85) cc_final: 0.7443 (mtm-85) REVERT: A 895 LYS cc_start: 0.7846 (pttp) cc_final: 0.7535 (ptmt) REVERT: A 959 LYS cc_start: 0.8122 (mttt) cc_final: 0.7710 (mtmt) REVERT: A 1000 GLN cc_start: 0.8215 (mt0) cc_final: 0.7937 (mt0) REVERT: A 1097 ASP cc_start: 0.7568 (m-30) cc_final: 0.7237 (p0) REVERT: A 1104 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7039 (mp0) REVERT: A 1155 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7934 (tp30) REVERT: A 1255 THR cc_start: 0.6165 (m) cc_final: 0.5886 (p) REVERT: A 1366 ASN cc_start: 0.8538 (p0) cc_final: 0.8318 (p0) REVERT: B 194 LYS cc_start: 0.7919 (mptt) cc_final: 0.7419 (ttpp) REVERT: C 113 MET cc_start: 0.3513 (ppp) cc_final: 0.3195 (ptp) REVERT: C 154 GLU cc_start: 0.8227 (tp30) cc_final: 0.7950 (tp30) outliers start: 39 outliers final: 15 residues processed: 241 average time/residue: 0.5904 time to fit residues: 154.4791 Evaluate side-chains 208 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 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 63 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 GLN A1158 ASN A1270 ASN A1322 ASN A1338 ASN A1374 ASN B 254 GLN C 161 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.160399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.122789 restraints weight = 15881.549| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.98 r_work: 0.3206 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13942 Z= 0.179 Angle : 0.597 9.783 18893 Z= 0.313 Chirality : 0.043 0.156 2108 Planarity : 0.005 0.049 2404 Dihedral : 4.709 28.813 1836 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.26 % Allowed : 11.97 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.20), residues: 1682 helix: 1.24 (0.18), residues: 861 sheet: 1.30 (0.51), residues: 90 loop : -0.98 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 855 TYR 0.018 0.002 TYR A 803 PHE 0.019 0.002 PHE A 372 TRP 0.009 0.001 TRP A 108 HIS 0.007 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00428 (13939) covalent geometry : angle 0.59736 (18893) hydrogen bonds : bond 0.06530 ( 684) hydrogen bonds : angle 4.36157 ( 1932) metal coordination : bond 0.00208 ( 3) *********************** 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 239 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.7757 (mmm160) cc_final: 0.7360 (mmt180) REVERT: A 196 LYS cc_start: 0.7423 (mptt) cc_final: 0.6941 (mmtm) REVERT: A 229 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7035 (tt0) REVERT: A 289 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7957 (ttm) REVERT: A 390 ASP cc_start: 0.7441 (m-30) cc_final: 0.7080 (t70) REVERT: A 536 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7035 (tp30) REVERT: A 542 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8082 (mm-30) REVERT: A 564 ARG cc_start: 0.8470 (mtp180) cc_final: 0.8093 (mtm180) REVERT: A 581 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7198 (tp30) REVERT: A 628 ARG cc_start: 0.8669 (tpt-90) cc_final: 0.8405 (mmt90) REVERT: A 696 ASN cc_start: 0.7584 (t0) cc_final: 0.7255 (m-40) REVERT: A 742 VAL cc_start: 0.8178 (t) cc_final: 0.7937 (p) REVERT: A 770 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7630 (mp) REVERT: A 785 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.8221 (m-80) REVERT: A 794 GLU cc_start: 0.8313 (mp0) cc_final: 0.8073 (mp0) REVERT: A 824 ARG cc_start: 0.8019 (mtp85) cc_final: 0.7417 (mtm180) REVERT: A 832 ILE cc_start: 0.7777 (mt) cc_final: 0.7473 (mm) REVERT: A 894 LYS cc_start: 0.8782 (mtpp) cc_final: 0.8342 (mmtt) REVERT: A 895 LYS cc_start: 0.7633 (pttp) cc_final: 0.7324 (ptmt) REVERT: A 959 LYS cc_start: 0.8117 (mttt) cc_final: 0.7705 (mtmt) REVERT: A 1000 GLN cc_start: 0.8218 (mt0) cc_final: 0.7890 (mt0) REVERT: A 1040 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.7533 (mtt-85) REVERT: A 1104 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7035 (mt-10) REVERT: A 1155 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7857 (tp30) REVERT: A 1255 THR cc_start: 0.6190 (OUTLIER) cc_final: 0.5932 (p) REVERT: A 1366 ASN cc_start: 0.8523 (p0) cc_final: 0.8321 (p0) REVERT: A 1385 TYR cc_start: 0.7491 (m-80) cc_final: 0.7235 (m-10) REVERT: A 1403 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6909 (pt0) REVERT: B 194 LYS cc_start: 0.7907 (mptt) cc_final: 0.7381 (ttpp) REVERT: C 113 MET cc_start: 0.3356 (ppp) cc_final: 0.3061 (ptp) REVERT: C 154 GLU cc_start: 0.8308 (tp30) cc_final: 0.7879 (tp30) outliers start: 49 outliers final: 20 residues processed: 221 average time/residue: 0.6052 time to fit residues: 145.2995 Evaluate side-chains 202 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 178 THR 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 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 542 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 770 LEU 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 985 THR Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1109 THR 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 1255 THR Chi-restraints excluded: chain A residue 1266 ILE 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 26 optimal weight: 0.3980 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 994 ASN A1048 GLN A1158 ASN A1270 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 = 0.3878 r_free = 0.3878 target = 0.161739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.124141 restraints weight = 15706.403| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.97 r_work: 0.3231 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13942 Z= 0.140 Angle : 0.551 9.507 18893 Z= 0.286 Chirality : 0.041 0.156 2108 Planarity : 0.004 0.049 2404 Dihedral : 4.524 29.171 1836 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.12 % Allowed : 13.76 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.20), residues: 1682 helix: 1.35 (0.18), residues: 872 sheet: 1.36 (0.51), residues: 91 loop : -0.96 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 271 TYR 0.018 0.001 TYR A 803 PHE 0.018 0.002 PHE A 414 TRP 0.008 0.001 TRP A 261 HIS 0.005 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00326 (13939) covalent geometry : angle 0.55116 (18893) hydrogen bonds : bond 0.05535 ( 684) hydrogen bonds : angle 4.22960 ( 1932) metal coordination : bond 0.00109 ( 3) *********************** 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 223 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7642 (mp) REVERT: A 41 ARG cc_start: 0.7735 (mmm160) cc_final: 0.7345 (mmt180) REVERT: A 51 ARG cc_start: 0.8322 (ptm160) cc_final: 0.7792 (ptt-90) REVERT: A 196 LYS cc_start: 0.7397 (mptt) cc_final: 0.6928 (mmtm) REVERT: A 217 ARG cc_start: 0.7393 (mpt180) cc_final: 0.7138 (mpt180) REVERT: A 229 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7035 (tt0) REVERT: A 390 ASP cc_start: 0.7404 (m-30) cc_final: 0.7080 (t70) REVERT: A 426 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7338 (mt0) REVERT: A 536 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7199 (tp30) REVERT: A 542 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8049 (mm-30) REVERT: A 564 ARG cc_start: 0.8444 (mtp180) cc_final: 0.8217 (mmm-85) REVERT: A 581 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7225 (tp30) REVERT: A 628 ARG cc_start: 0.8621 (tpt-90) cc_final: 0.8370 (mmt90) REVERT: A 634 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.7446 (p) REVERT: A 696 ASN cc_start: 0.7600 (t0) cc_final: 0.7244 (m-40) REVERT: A 742 VAL cc_start: 0.8143 (t) cc_final: 0.7911 (p) REVERT: A 770 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7671 (mp) REVERT: A 785 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.8224 (m-80) REVERT: A 791 LYS cc_start: 0.7675 (mtpp) cc_final: 0.7461 (mtpp) REVERT: A 794 GLU cc_start: 0.8386 (mp0) cc_final: 0.8091 (mp0) REVERT: A 824 ARG cc_start: 0.8000 (mtp85) cc_final: 0.7385 (mtm180) REVERT: A 895 LYS cc_start: 0.7583 (pttp) cc_final: 0.7254 (ptmt) REVERT: A 925 TYR cc_start: 0.9098 (OUTLIER) cc_final: 0.7937 (p90) REVERT: A 959 LYS cc_start: 0.8072 (mttt) cc_final: 0.7675 (mtmt) REVERT: A 962 LEU cc_start: 0.7554 (mt) cc_final: 0.7311 (pp) REVERT: A 1000 GLN cc_start: 0.8155 (mt0) cc_final: 0.7826 (mt0) REVERT: A 1040 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7506 (mtt-85) REVERT: A 1104 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7005 (mt-10) REVERT: A 1143 GLU cc_start: 0.7817 (pt0) cc_final: 0.7379 (mt-10) REVERT: A 1155 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7810 (tp30) REVERT: A 1374 ASN cc_start: 0.8035 (m-40) cc_final: 0.7655 (m110) REVERT: A 1403 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6919 (pt0) REVERT: B 194 LYS cc_start: 0.7880 (mptt) cc_final: 0.7329 (ttpp) REVERT: C 113 MET cc_start: 0.3600 (ppp) cc_final: 0.3266 (ptp) REVERT: C 154 GLU cc_start: 0.8289 (tp30) cc_final: 0.7893 (tp30) outliers start: 47 outliers final: 23 residues processed: 205 average time/residue: 0.6167 time to fit residues: 138.3883 Evaluate side-chains 204 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 187 ASP 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 542 GLU Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 737 LYS 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 925 TYR 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 1241 LEU Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 213 LEU 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 96 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 144 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 ASN ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 GLN A1158 ASN A1270 ASN A1322 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 = 0.3839 r_free = 0.3839 target = 0.158280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.120109 restraints weight = 15877.411| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.03 r_work: 0.3175 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13942 Z= 0.208 Angle : 0.618 10.039 18893 Z= 0.321 Chirality : 0.044 0.160 2108 Planarity : 0.005 0.051 2404 Dihedral : 4.698 30.977 1836 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.66 % Allowed : 13.83 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.20), residues: 1682 helix: 1.17 (0.18), residues: 868 sheet: 1.09 (0.50), residues: 97 loop : -0.96 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 855 TYR 0.022 0.002 TYR A1385 PHE 0.025 0.002 PHE A 414 TRP 0.010 0.001 TRP A 108 HIS 0.006 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00513 (13939) covalent geometry : angle 0.61836 (18893) hydrogen bonds : bond 0.06973 ( 684) hydrogen bonds : angle 4.36525 ( 1932) metal coordination : bond 0.00465 ( 3) *********************** 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 230 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 175 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7741 (mp) REVERT: A 41 ARG cc_start: 0.7841 (mmm160) cc_final: 0.7405 (mmt180) REVERT: A 51 ARG cc_start: 0.8320 (ptm160) cc_final: 0.7822 (ptt-90) REVERT: A 196 LYS cc_start: 0.7478 (mptt) cc_final: 0.6960 (mmtm) REVERT: A 229 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7041 (tt0) REVERT: A 289 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7846 (ttm) REVERT: A 390 ASP cc_start: 0.7462 (m-30) cc_final: 0.7133 (t70) REVERT: A 521 GLU cc_start: 0.7191 (mp0) cc_final: 0.6988 (mp0) REVERT: A 536 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7315 (tp30) REVERT: A 542 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8096 (mm-30) REVERT: A 564 ARG cc_start: 0.8508 (mtp180) cc_final: 0.8177 (mtm180) REVERT: A 581 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7266 (tp30) REVERT: A 696 ASN cc_start: 0.7715 (t0) cc_final: 0.7474 (m110) REVERT: A 770 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7763 (mp) REVERT: A 785 TYR cc_start: 0.9141 (OUTLIER) cc_final: 0.8471 (m-80) REVERT: A 794 GLU cc_start: 0.8417 (mp0) cc_final: 0.8183 (mp0) REVERT: A 824 ARG cc_start: 0.8077 (mtp85) cc_final: 0.7426 (mtm180) REVERT: A 895 LYS cc_start: 0.7560 (pttp) cc_final: 0.7230 (ptmt) REVERT: A 925 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.7931 (p90) REVERT: A 959 LYS cc_start: 0.8059 (mttt) cc_final: 0.7597 (mtmt) REVERT: A 962 LEU cc_start: 0.7607 (mt) cc_final: 0.7367 (pp) REVERT: A 1000 GLN cc_start: 0.8206 (mt0) cc_final: 0.7792 (mt0) REVERT: A 1040 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.7663 (mtt-85) REVERT: A 1104 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7106 (mt-10) REVERT: A 1143 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: A 1155 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7921 (tp30) REVERT: A 1255 THR cc_start: 0.6312 (m) cc_final: 0.6089 (p) REVERT: A 1403 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6907 (pt0) REVERT: B 194 LYS cc_start: 0.7939 (mptt) cc_final: 0.7390 (ttpp) REVERT: B 254 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: C 113 MET cc_start: 0.3593 (ppp) cc_final: 0.3245 (ptp) REVERT: C 154 GLU cc_start: 0.8284 (tp30) cc_final: 0.7979 (tp30) outliers start: 55 outliers final: 29 residues processed: 208 average time/residue: 0.5930 time to fit residues: 134.6268 Evaluate side-chains 209 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 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 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 1266 ILE 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 213 LEU Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 267 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 8 optimal weight: 0.0570 chunk 39 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 162 optimal weight: 0.0170 chunk 86 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.6136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 GLN A1048 GLN 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 = 0.3899 r_free = 0.3899 target = 0.164031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.126377 restraints weight = 15720.647| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.99 r_work: 0.3281 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13942 Z= 0.104 Angle : 0.504 8.247 18893 Z= 0.261 Chirality : 0.040 0.160 2108 Planarity : 0.004 0.049 2404 Dihedral : 4.277 27.498 1836 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.46 % Allowed : 16.02 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.20), residues: 1682 helix: 1.60 (0.18), residues: 868 sheet: 1.15 (0.49), residues: 97 loop : -0.81 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 294 TYR 0.016 0.001 TYR A 237 PHE 0.013 0.001 PHE A 414 TRP 0.011 0.001 TRP A 76 HIS 0.004 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00216 (13939) covalent geometry : angle 0.50361 (18893) hydrogen bonds : bond 0.04351 ( 684) hydrogen bonds : angle 4.09156 ( 1932) metal coordination : bond 0.00273 ( 3) *********************** 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 224 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.7729 (mmm160) cc_final: 0.7325 (mmt180) REVERT: A 51 ARG cc_start: 0.8247 (ptm160) cc_final: 0.7759 (ptt-90) REVERT: A 196 LYS cc_start: 0.7386 (mptt) cc_final: 0.6867 (mmtm) REVERT: A 229 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7007 (tt0) REVERT: A 426 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7201 (mp10) REVERT: A 431 LYS cc_start: 0.7618 (tptp) cc_final: 0.7275 (mptt) REVERT: A 536 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7058 (tp30) REVERT: A 542 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8046 (mm-30) REVERT: A 564 ARG cc_start: 0.8404 (mtp180) cc_final: 0.8167 (mmm-85) REVERT: A 581 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7165 (tp30) REVERT: A 696 ASN cc_start: 0.7676 (t0) cc_final: 0.7441 (m110) REVERT: A 791 LYS cc_start: 0.7638 (mtpp) cc_final: 0.7136 (mttt) REVERT: A 824 ARG cc_start: 0.7996 (mtp85) cc_final: 0.7348 (mtm180) REVERT: A 895 LYS cc_start: 0.7416 (pttp) cc_final: 0.7099 (ptmt) REVERT: A 925 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.7882 (p90) REVERT: A 959 LYS cc_start: 0.8079 (mttt) cc_final: 0.7673 (mtmt) REVERT: A 962 LEU cc_start: 0.7541 (mt) cc_final: 0.7307 (pp) REVERT: A 1000 GLN cc_start: 0.8108 (mt0) cc_final: 0.7786 (mt0) REVERT: A 1040 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.7663 (mtt-85) REVERT: A 1104 GLU cc_start: 0.7544 (mm-30) cc_final: 0.6997 (mt-10) REVERT: A 1143 GLU cc_start: 0.7846 (pt0) cc_final: 0.7370 (mt-10) REVERT: A 1155 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7831 (tp30) REVERT: B 194 LYS cc_start: 0.7863 (mptt) cc_final: 0.7278 (ttpp) REVERT: C 113 MET cc_start: 0.3581 (ppp) cc_final: 0.3218 (ptp) REVERT: C 154 GLU cc_start: 0.8182 (tp30) cc_final: 0.7832 (tp30) outliers start: 37 outliers final: 17 residues processed: 211 average time/residue: 0.5769 time to fit residues: 133.0875 Evaluate side-chains 196 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 737 LYS Chi-restraints excluded: chain A residue 753 SER 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 1040 ARG Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1188 ASN Chi-restraints excluded: chain A residue 1252 LEU 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 Chi-restraints excluded: chain D residue 134 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 105 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 48 optimal weight: 0.0770 chunk 121 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 overall best weight: 1.5144 ------------------------------------------------------------------------------- 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 A1270 ASN A1322 ASN C 161 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.161938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.124205 restraints weight = 15686.347| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.03 r_work: 0.3241 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3332 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= 0.131 Angle : 0.526 8.744 18893 Z= 0.272 Chirality : 0.041 0.159 2108 Planarity : 0.004 0.049 2404 Dihedral : 4.265 27.801 1836 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.59 % Allowed : 16.16 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.20), residues: 1682 helix: 1.60 (0.18), residues: 872 sheet: 1.19 (0.49), residues: 97 loop : -0.79 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1057 TYR 0.015 0.001 TYR A 803 PHE 0.018 0.002 PHE A 414 TRP 0.008 0.001 TRP A 261 HIS 0.005 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00303 (13939) covalent geometry : angle 0.52642 (18893) hydrogen bonds : bond 0.05089 ( 684) hydrogen bonds : angle 4.10344 ( 1932) metal coordination : bond 0.00192 ( 3) *********************** 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 214 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7610 (mp) REVERT: A 41 ARG cc_start: 0.7749 (mmm160) cc_final: 0.7326 (mmt180) REVERT: A 51 ARG cc_start: 0.8282 (ptm160) cc_final: 0.7773 (ptt-90) REVERT: A 196 LYS cc_start: 0.7407 (mptt) cc_final: 0.6868 (mmtm) REVERT: A 229 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7036 (tt0) REVERT: A 390 ASP cc_start: 0.7374 (m-30) cc_final: 0.7058 (t70) REVERT: A 431 LYS cc_start: 0.7634 (tptp) cc_final: 0.7285 (mptt) REVERT: A 536 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7088 (tp30) REVERT: A 564 ARG cc_start: 0.8447 (mtp180) cc_final: 0.8181 (mmm-85) REVERT: A 581 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7207 (tp30) REVERT: A 696 ASN cc_start: 0.7592 (t0) cc_final: 0.7382 (m110) REVERT: A 770 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7647 (mp) REVERT: A 791 LYS cc_start: 0.7636 (mtpp) cc_final: 0.7124 (mttt) REVERT: A 824 ARG cc_start: 0.8008 (mtp85) cc_final: 0.7352 (mtm180) REVERT: A 877 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7764 (tp40) REVERT: A 895 LYS cc_start: 0.7421 (pttp) cc_final: 0.7107 (ptmt) REVERT: A 925 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.7913 (p90) REVERT: A 959 LYS cc_start: 0.8078 (mttt) cc_final: 0.7624 (mtmt) REVERT: A 962 LEU cc_start: 0.7571 (mt) cc_final: 0.7325 (pp) REVERT: A 1000 GLN cc_start: 0.8115 (mt0) cc_final: 0.7801 (mt0) REVERT: A 1073 MET cc_start: 0.6688 (tpt) cc_final: 0.6457 (tpt) REVERT: A 1104 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7001 (mt-10) REVERT: A 1143 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: A 1155 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7847 (tp30) REVERT: B 194 LYS cc_start: 0.7939 (mptt) cc_final: 0.7306 (ttpp) REVERT: C 113 MET cc_start: 0.3670 (ppp) cc_final: 0.3314 (ptp) REVERT: C 154 GLU cc_start: 0.8289 (tp30) cc_final: 0.7880 (tp30) outliers start: 39 outliers final: 19 residues processed: 200 average time/residue: 0.6133 time to fit residues: 133.7147 Evaluate side-chains 193 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 199 ILE 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 640 ASN Chi-restraints excluded: chain A residue 737 LYS 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 877 GLN Chi-restraints excluded: chain A residue 925 TYR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1188 ASN Chi-restraints excluded: chain A residue 1252 LEU 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 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 108 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 114 optimal weight: 0.0970 chunk 110 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.7582 ------------------------------------------------------------------------------- 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 A1270 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 = 0.3870 r_free = 0.3870 target = 0.161286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.123426 restraints weight = 15680.675| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.03 r_work: 0.3224 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3397 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= 0.142 Angle : 0.549 12.087 18893 Z= 0.281 Chirality : 0.041 0.156 2108 Planarity : 0.004 0.050 2404 Dihedral : 4.320 28.267 1836 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.93 % Allowed : 16.16 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.20), residues: 1682 helix: 1.54 (0.18), residues: 872 sheet: 1.20 (0.50), residues: 97 loop : -0.78 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 628 TYR 0.016 0.001 TYR A 803 PHE 0.020 0.002 PHE A 414 TRP 0.007 0.001 TRP A 76 HIS 0.005 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00335 (13939) covalent geometry : angle 0.54860 (18893) hydrogen bonds : bond 0.05434 ( 684) hydrogen bonds : angle 4.15260 ( 1932) metal coordination : bond 0.00256 ( 3) *********************** 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 215 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7630 (mp) REVERT: A 41 ARG cc_start: 0.7754 (mmm160) cc_final: 0.7330 (mmt180) REVERT: A 51 ARG cc_start: 0.8230 (ptm160) cc_final: 0.7714 (ptt-90) REVERT: A 196 LYS cc_start: 0.7455 (mptt) cc_final: 0.6933 (mmtm) REVERT: A 229 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7060 (tt0) REVERT: A 390 ASP cc_start: 0.7405 (m-30) cc_final: 0.7075 (t70) REVERT: A 431 LYS cc_start: 0.7628 (tptp) cc_final: 0.7272 (mptt) REVERT: A 536 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7129 (tp30) REVERT: A 581 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7222 (tp30) REVERT: A 696 ASN cc_start: 0.7654 (t0) cc_final: 0.7388 (m110) REVERT: A 770 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7683 (mp) REVERT: A 824 ARG cc_start: 0.8031 (mtp85) cc_final: 0.7369 (mtm180) REVERT: A 895 LYS cc_start: 0.7363 (pttp) cc_final: 0.7045 (ptmt) REVERT: A 925 TYR cc_start: 0.9119 (OUTLIER) cc_final: 0.7829 (p90) REVERT: A 959 LYS cc_start: 0.8058 (mttt) cc_final: 0.7599 (mtmt) REVERT: A 962 LEU cc_start: 0.7614 (mt) cc_final: 0.7383 (pp) REVERT: A 1104 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7004 (mt-10) REVERT: A 1143 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7371 (mt-10) REVERT: A 1155 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7867 (tp30) REVERT: A 1255 THR cc_start: 0.6259 (OUTLIER) cc_final: 0.5986 (p) REVERT: A 1403 GLU cc_start: 0.7774 (pt0) cc_final: 0.7282 (pt0) REVERT: B 194 LYS cc_start: 0.7908 (mptt) cc_final: 0.7314 (ttpp) REVERT: C 113 MET cc_start: 0.3641 (OUTLIER) cc_final: 0.3284 (ptp) REVERT: C 154 GLU cc_start: 0.8273 (tp30) cc_final: 0.7861 (tp30) outliers start: 44 outliers final: 21 residues processed: 198 average time/residue: 0.5873 time to fit residues: 127.1187 Evaluate side-chains 195 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 195 VAL 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 634 THR Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 737 LYS 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 1014 LEU Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1188 ASN Chi-restraints excluded: chain A residue 1255 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 113 MET 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 139 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 125 optimal weight: 0.0270 chunk 30 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 48 optimal weight: 0.0060 chunk 18 optimal weight: 3.9990 overall best weight: 1.6060 ------------------------------------------------------------------------------- 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 A1270 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 = 0.3874 r_free = 0.3874 target = 0.161664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.123898 restraints weight = 15632.768| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.99 r_work: 0.3229 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3448 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= 0.135 Angle : 0.545 13.108 18893 Z= 0.278 Chirality : 0.041 0.157 2108 Planarity : 0.004 0.049 2404 Dihedral : 4.274 28.124 1836 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.59 % Allowed : 16.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.20), residues: 1682 helix: 1.55 (0.18), residues: 872 sheet: 1.22 (0.50), residues: 97 loop : -0.77 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 628 TYR 0.016 0.001 TYR A 803 PHE 0.019 0.002 PHE A 414 TRP 0.008 0.001 TRP A 76 HIS 0.005 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00316 (13939) covalent geometry : angle 0.54511 (18893) hydrogen bonds : bond 0.05237 ( 684) hydrogen bonds : angle 4.13815 ( 1932) metal coordination : bond 0.00188 ( 3) *********************** 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 210 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7592 (mp) REVERT: A 41 ARG cc_start: 0.7761 (mmm160) cc_final: 0.7331 (mmt180) REVERT: A 51 ARG cc_start: 0.8237 (ptm160) cc_final: 0.7721 (ptt-90) REVERT: A 196 LYS cc_start: 0.7479 (mptt) cc_final: 0.6986 (mmtm) REVERT: A 217 ARG cc_start: 0.7403 (mpt180) cc_final: 0.7122 (mpt180) REVERT: A 390 ASP cc_start: 0.7435 (m-30) cc_final: 0.7120 (t70) REVERT: A 431 LYS cc_start: 0.7645 (tptp) cc_final: 0.7298 (mptt) REVERT: A 536 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7151 (tp30) REVERT: A 581 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7253 (tp30) REVERT: A 696 ASN cc_start: 0.7640 (t0) cc_final: 0.7370 (m110) REVERT: A 791 LYS cc_start: 0.7870 (mtpp) cc_final: 0.7332 (mttt) REVERT: A 824 ARG cc_start: 0.8030 (mtp85) cc_final: 0.7392 (mtm180) REVERT: A 895 LYS cc_start: 0.7364 (pttp) cc_final: 0.7048 (ptmt) REVERT: A 925 TYR cc_start: 0.9123 (OUTLIER) cc_final: 0.7850 (p90) REVERT: A 959 LYS cc_start: 0.8068 (mttt) cc_final: 0.7609 (mtmt) REVERT: A 1000 GLN cc_start: 0.8177 (mt0) cc_final: 0.7745 (mt0) REVERT: A 1073 MET cc_start: 0.6786 (tpt) cc_final: 0.6560 (tpt) REVERT: A 1104 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7016 (mt-10) REVERT: A 1143 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: A 1155 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7879 (tp30) REVERT: A 1255 THR cc_start: 0.6305 (OUTLIER) cc_final: 0.6042 (p) REVERT: B 194 LYS cc_start: 0.7938 (mptt) cc_final: 0.7343 (ttpp) REVERT: B 254 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8080 (tt0) REVERT: C 113 MET cc_start: 0.3494 (OUTLIER) cc_final: 0.3151 (ptp) REVERT: C 154 GLU cc_start: 0.8257 (tp30) cc_final: 0.7864 (tp30) outliers start: 39 outliers final: 23 residues processed: 195 average time/residue: 0.5484 time to fit residues: 117.2232 Evaluate side-chains 199 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 195 VAL Chi-restraints excluded: chain A residue 232 VAL 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 634 THR Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 737 LYS 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 1014 LEU Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1188 ASN Chi-restraints excluded: chain A residue 1255 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 B residue 254 GLN Chi-restraints excluded: chain C residue 113 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 44 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 154 optimal weight: 0.0970 chunk 55 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 A1270 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 = 0.3874 r_free = 0.3874 target = 0.161658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.123865 restraints weight = 15659.125| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.99 r_work: 0.3231 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3514 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= 0.134 Angle : 0.544 11.605 18893 Z= 0.278 Chirality : 0.041 0.156 2108 Planarity : 0.004 0.051 2404 Dihedral : 4.261 28.096 1836 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.26 % Allowed : 17.09 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.20), residues: 1682 helix: 1.61 (0.18), residues: 866 sheet: 1.18 (0.50), residues: 97 loop : -0.79 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 628 TYR 0.015 0.001 TYR A 803 PHE 0.019 0.002 PHE A 414 TRP 0.008 0.001 TRP A 76 HIS 0.005 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00315 (13939) covalent geometry : angle 0.54381 (18893) hydrogen bonds : bond 0.05242 ( 684) hydrogen bonds : angle 4.14046 ( 1932) metal coordination : bond 0.00205 ( 3) ********************** 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 205 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7593 (mp) REVERT: A 41 ARG cc_start: 0.7716 (mmm160) cc_final: 0.7282 (mmp-170) REVERT: A 51 ARG cc_start: 0.8236 (ptm160) cc_final: 0.7725 (ptt-90) REVERT: A 196 LYS cc_start: 0.7487 (mptt) cc_final: 0.6993 (mmtm) REVERT: A 217 ARG cc_start: 0.7414 (mpt180) cc_final: 0.7169 (mpt180) REVERT: A 390 ASP cc_start: 0.7431 (m-30) cc_final: 0.7119 (t70) REVERT: A 431 LYS cc_start: 0.7640 (tptp) cc_final: 0.7289 (mptt) REVERT: A 536 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7242 (tp30) REVERT: A 581 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7248 (tp30) REVERT: A 696 ASN cc_start: 0.7650 (t0) cc_final: 0.7372 (m110) REVERT: A 770 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7691 (mp) REVERT: A 791 LYS cc_start: 0.7908 (mtpp) cc_final: 0.7339 (mttt) REVERT: A 824 ARG cc_start: 0.8035 (mtp85) cc_final: 0.7384 (mtm180) REVERT: A 895 LYS cc_start: 0.7352 (pttp) cc_final: 0.7034 (ptmt) REVERT: A 925 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.7858 (p90) REVERT: A 927 ASN cc_start: 0.8615 (m110) cc_final: 0.8368 (m-40) REVERT: A 959 LYS cc_start: 0.8063 (mttt) cc_final: 0.7639 (mtmt) REVERT: A 1000 GLN cc_start: 0.8175 (mt0) cc_final: 0.7735 (mt0) REVERT: A 1104 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7029 (mt-10) REVERT: A 1143 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7423 (mt-10) REVERT: A 1155 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7871 (tp30) REVERT: A 1255 THR cc_start: 0.6305 (OUTLIER) cc_final: 0.6014 (p) REVERT: B 194 LYS cc_start: 0.7940 (mptt) cc_final: 0.7370 (ttpp) REVERT: B 254 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: C 113 MET cc_start: 0.3466 (ppp) cc_final: 0.3118 (ptp) REVERT: C 154 GLU cc_start: 0.8238 (tp30) cc_final: 0.7850 (tp30) outliers start: 34 outliers final: 23 residues processed: 191 average time/residue: 0.5535 time to fit residues: 115.5826 Evaluate side-chains 196 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 195 VAL Chi-restraints excluded: chain A residue 232 VAL 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 634 THR Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 737 LYS 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 851 THR Chi-restraints excluded: chain A residue 925 TYR Chi-restraints excluded: chain A residue 985 THR 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 1143 GLU Chi-restraints excluded: chain A residue 1188 ASN Chi-restraints excluded: chain A residue 1255 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 B residue 254 GLN 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 36 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 54 optimal weight: 0.2980 chunk 67 optimal weight: 0.0670 chunk 118 optimal weight: 0.0060 chunk 7 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 121 optimal weight: 0.2980 chunk 151 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 overall best weight: 0.3334 ------------------------------------------------------------------------------- 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 A1270 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 = 0.3934 r_free = 0.3934 target = 0.167472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.130512 restraints weight = 15630.909| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.97 r_work: 0.3347 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13942 Z= 0.093 Angle : 0.500 13.533 18893 Z= 0.253 Chirality : 0.039 0.158 2108 Planarity : 0.004 0.047 2404 Dihedral : 3.919 23.220 1836 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.53 % Allowed : 17.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.21), residues: 1682 helix: 1.95 (0.18), residues: 854 sheet: 1.25 (0.49), residues: 97 loop : -0.66 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 564 TYR 0.016 0.001 TYR A 237 PHE 0.016 0.001 PHE A 529 TRP 0.011 0.001 TRP A 76 HIS 0.002 0.000 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00192 (13939) covalent geometry : angle 0.50011 (18893) hydrogen bonds : bond 0.03438 ( 684) hydrogen bonds : angle 3.96796 ( 1932) metal coordination : bond 0.00428 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4793.23 seconds wall clock time: 82 minutes 26.54 seconds (4946.54 seconds total)